[gentoo-commits] proj/sci:master commit in: sci-biology/consed/
commit: 1efa11df584f6796903837ee2272ea628686889d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Apr 5 11:38:06 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 5 11:38:06 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1efa11df
sci-biology/consed: fix more hardcoded paths
Package-Manager: portage-2.2.7
---
sci-biology/consed/ChangeLog | 5 +
sci-biology/consed/consed-20-r1.ebuild | 4 +++-
sci-biology/consed/consed-21.ebuild| 4 +++-
sci-biology/consed/consed-22.ebuild| 4 +++-
sci-biology/consed/consed-23.ebuild| 4 +++-
sci-biology/consed/consed-24.ebuild| 4 +++-
sci-biology/consed/consed-25.ebuild| 4 +++-
sci-biology/consed/consed-26.ebuild| 4 +++-
sci-biology/consed/consed-27.ebuild| 4 +++-
9 files changed, 29 insertions(+), 8 deletions(-)
diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 0fe8c19..ed7f9c8 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 05 Apr 2014; Martin Mokrejs
consed-20-r1.ebuild,
+ consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
+ consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
+ sci-biology/consed: fix more hardcoded paths
+
02 Apr 2014; Martin Mokrejs
consed-20-r1.ebuild,
consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
diff --git a/sci-biology/consed/consed-20-r1.ebuild
b/sci-biology/consed/consed-20-r1.ebuild
index cfcb66e..7f7ddc1 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -65,7 +65,9 @@ src_install() {
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
doenvd "${S}/99consed" || die
- sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
|| die
+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+ sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
+ sed -e 's#/wt1/gordon/genome#/usr/bin#' -i
"${D}"/usr/bin/fastq2Phrap.perl || die
dodoc README.txt *_announcement.txt || die
}
diff --git a/sci-biology/consed/consed-21.ebuild
b/sci-biology/consed/consed-21.ebuild
index 55ba90a..77ec1a2 100644
--- a/sci-biology/consed/consed-21.ebuild
+++ b/sci-biology/consed/consed-21.ebuild
@@ -64,7 +64,9 @@ src_install() {
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
- sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
|| die
+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+ sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
+ sed -e 's#/wt1/gordon/genome#/usr/bin#' -i
"${D}"/usr/bin/fastq2Phrap.perl || die
doenvd "${S}/99consed" || die
dodoc README.txt *_announcement.txt || die
}
diff --git a/sci-biology/consed/consed-22.ebuild
b/sci-biology/consed/consed-22.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-22.ebuild
+++ b/sci-biology/consed/consed-22.ebuild
@@ -65,7 +65,9 @@ src_install() {
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
doenvd "${S}/99consed" || die
- sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
|| die
+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+ sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
+ sed -e 's#/wt1/gordon/genome#/usr/bin#' -i
"${D}"/usr/bin/fastq2Phrap.perl || die
dodoc README.txt *_announcement.txt || die
}
diff --git a/sci-biology/consed/consed-23.ebuild
b/sci-biology/consed/consed-23.ebuild
index d0a26
[gentoo-commits] proj/sci:master commit in: sci-biology/consed/
commit: ae0815f92cc318782734d09b18d0cf78f564c8bb
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Apr 5 13:19:25 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 5 13:19:25 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae0815f9
sci-biology/consed: add a stub file for consedrc; refer to it via
CONSED_PARAMETERS
Package-Manager: portage-2.2.7
---
sci-biology/consed/ChangeLog | 6 ++
sci-biology/consed/consed-20-r1.ebuild | 3 +++
sci-biology/consed/consed-21.ebuild| 3 +++
sci-biology/consed/consed-22.ebuild| 3 +++
sci-biology/consed/consed-23.ebuild| 3 +++
sci-biology/consed/consed-24.ebuild| 3 +++
sci-biology/consed/consed-25.ebuild| 3 +++
sci-biology/consed/consed-26.ebuild| 3 +++
sci-biology/consed/consed-27.ebuild| 3 +++
9 files changed, 30 insertions(+)
diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index ed7f9c8..4bbf7b9 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -5,6 +5,12 @@
05 Apr 2014; Martin Mokrejs
consed-20-r1.ebuild,
consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
+ sci-biology/consed: add a stub file for consedrc; refer to it via
+ CONSED_PARAMETERS
+
+ 05 Apr 2014; Martin Mokrejs
consed-20-r1.ebuild,
+ consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
+ consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
sci-biology/consed: fix more hardcoded paths
02 Apr 2014; Martin Mokrejs
consed-20-r1.ebuild,
diff --git a/sci-biology/consed/consed-20-r1.ebuild
b/sci-biology/consed/consed-20-r1.ebuild
index 7f7ddc1..30ba866 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -64,6 +64,9 @@ src_install() {
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+ echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+ mkdir -p "${D}"/etc/consedrc
+ touch "${D}"/etc/consedrc
doenvd "${S}/99consed" || die
sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
diff --git a/sci-biology/consed/consed-21.ebuild
b/sci-biology/consed/consed-21.ebuild
index 77ec1a2..b7993b7 100644
--- a/sci-biology/consed/consed-21.ebuild
+++ b/sci-biology/consed/consed-21.ebuild
@@ -64,6 +64,9 @@ src_install() {
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+ echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+ mkdir -p "${D}"/etc/consedrc
+ touch "${D}"/etc/consedrc
sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
sed -e 's#/wt1/gordon/genome#/usr/bin#' -i
"${D}"/usr/bin/fastq2Phrap.perl || die
diff --git a/sci-biology/consed/consed-22.ebuild
b/sci-biology/consed/consed-22.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-22.ebuild
+++ b/sci-biology/consed/consed-22.ebuild
@@ -64,6 +64,9 @@ src_install() {
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+ echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+ mkdir -p "${D}"/etc/consedrc
+ touch "${D}"/etc/consedrc
doenvd "${S}/99consed" || die
sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl
"${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i
"${D}"/usr/bin/phredPhrap || die
diff --git a/sci-biology/consed
[gentoo-commits] proj/sci:master commit in: sci-biology/mira/
commit: 97b1cf9bacba1cede303203987f487a1290bc60e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Apr 12 12:28:06 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 12 12:28:06 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=97b1cf9b
sci-biology/mira-4.0.1: bump to current recommended bugfix release
Package-Manager: portage-2.2.7
---
sci-biology/mira/ChangeLog | 5 +++
sci-biology/mira/mira-4.0.1.ebuild | 76 ++
2 files changed, 81 insertions(+)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 4dd3e5b..b5f200e 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mira-4.0.1 (12 Apr 2014)
+
+ 12 Apr 2014; Martin Mokrejs +mira-4.0.1.ebuild:
+ sci-biology/mira-4.0.1: bump to current recommended bugfix release
+
06 Jan 2014; Justin Lecher -mira-3.4.0.1.ebuild,
-mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild,
-mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild:
diff --git a/sci-biology/mira/mira-4.0.1.ebuild
b/sci-biology/mira/mira-4.0.1.ebuild
new file mode 100644
index 000..f9c38fa
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.1.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived)
to mira-4.0rc2 (upstream fromat)
+
+inherit autotools eutils multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454
and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html";
+SRC_URI="
+
http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
+
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+#
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+#
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc"
+
+CDEPEND="
+ dev-libs/boost
+ dev-util/google-perftools"
+DEPEND="${CDEPEND}
+ app-editors/vim-core
+ dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i
's/flex++/flex -+/' || die
+ epatch \
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
+
+ sed \
+ -e "s:-O[23]::g" \
+ -e "s:-funroll-loops::g" \
+ -i configure.ac || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+# base_src_compile
+# # TODO: resolve docbook incompatibility for building docs
+# if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+ default
+ dodoc ${DOCS[@]}
+
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+ dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo
"http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html";
+}
[gentoo-commits] proj/sci:master commit in: /
commit: 5cdf64649280508520fc9b96b6926e0ce2c0d283
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Apr 12 12:29:38 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 12 12:29:38 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5cdf6464
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
dev-python/ffnet/ChangeLog |6 +-
dev-python/ffnet/Manifest |2 +-
.../{ffnet-0.6.2.ebuild => ffnet-0.7.1.ebuild} | 23 +-
dev-python/ffnet/metadata.xml | 10 +-
sci-chemistry/gromacs/ChangeLog|8 +
sci-chemistry/gromacs/Manifest |4 +-
...cs-5.0_beta1.ebuild => gromacs-5.0..ebuild} | 50 +-
...{gromacs-.ebuild => gromacs-5.0_rc1.ebuild} | 43 +-
sci-chemistry/gromacs/gromacs-.ebuild | 39 +-
sci-chemistry/gromacs/metadata.xml | 11 +-
sci-libs/dcmtk/ChangeLog | 14 +-
sci-libs/dcmtk/Manifest|4 +-
sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild | 71 -
sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild | 79 -
sci-libs/dcmtk/dcmtk-3.6.0.ebuild | 72 +
sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch| 89 +
sci-libs/dcmtk/files/07_doxygen.patch | 1804
sci-libs/dcmtk/files/bug674361.patch | 1015 +++
sci-libs/dcmtk/files/dcmtk-asneeded.patch | 16 +
sci-libs/dcmtk/files/dcmtk_version_number.patch| 131 ++
sci-libs/dcmtk/files/doubledes.patch | 31 +
sci-libs/dcmtk/files/fixnull.patch | 36 +
sci-libs/dcmtk/files/noleak.patch | 36 +
sci-libs/dcmtk/files/nothrow.patch | 76 +
sci-libs/dcmtk/files/prefs.patch | 26 +
.../files/regression_stacksequenceisodd.patch | 98 ++
.../dcmtk/files/use_correct_number_of_TS.patch | 19 +
sci-libs/dcmtk/metadata.xml| 30 +-
sci-libs/itk/ChangeLog | 11 +
sci-libs/itk/Manifest |2 +
...p-TransformFileReader-TransformFileWriter.patch | 50 +
...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch | 28 +
...itkGradientDescentOptimizerv4-wrapping-wa.patch | 73 +
...OptimizerParameterScalesEstimatorTemplate.patch | 30 +
.../0005-make-gdcm-helper-library-static.patch | 11 +
sci-libs/itk/files/nrrdio-linking.patch| 15 +
.../itk/{itk-4.4.2-r1.ebuild => itk-4.5.1.ebuild} | 76 +-
sci-mathematics/pulp/ChangeLog |6 +-
sci-mathematics/pulp/Manifest |2 +-
.../pulp/{pulp-1.5.3.ebuild => pulp-1.5.6.ebuild} | 16 +-
sci-visualization/visit/visit-2.7.2.ebuild |6 +
41 files changed, 3872 insertions(+), 297 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
commit: 34c1dd0d45a5787936bd8ee86afbdf8f21138f55
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 08:51:30 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 08:51:30 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34c1dd0d
sci-biology/barrnap: new package, package contains bundled binaries, untested
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 9 +
sci-biology/barrnap/barrnap-0.3.ebuild | 22 ++
sci-biology/barrnap/metadata.xml | 9 +
3 files changed, 40 insertions(+)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
new file mode 100644
index 000..df39571
--- /dev/null
+++ b/sci-biology/barrnap/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/barrnap
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*barrnap-0.3 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs
+barrnap-0.3.ebuild,
+ +metadata.xml:
+ sci-biology/barrnap: new package, package contains bundled binaries, untested
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild
b/sci-biology/barrnap/barrnap-0.3.ebuild
new file mode 100644
index 000..f5af3ab
--- /dev/null
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3
format"
+HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml";
+SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz";
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled binaries of hmmer-3.1 (dev version)
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/nesoni"
diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/barrnap/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: /
commit: 51745b131d5c80ef70624b1e835ea763050c12d8 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Apr 15 08:52:08 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Apr 15 08:52:08 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=51745b13 Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci app-editors/neovim/neovim-.ebuild | 1 + sci-chemistry/gromacs/ChangeLog | 4 sci-chemistry/gromacs/gromacs-5.0..ebuild | 12 ++-- sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild | 12 ++-- sci-chemistry/gromacs/gromacs-.ebuild | 12 ++-- sci-chemistry/gromacs/metadata.xml| 1 + 6 files changed, 36 insertions(+), 6 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/nesoni/
commit: e6aadf2268b6d9cb675653b9c8e3717ca2597298
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 08:55:06 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 08:55:06 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e6aadf22
sci-biology/nesoni: new package, needs some dev-lang/R -based packages to be
installed
Package-Manager: portage-2.2.7
---
sci-biology/nesoni/ChangeLog | 10 ++
sci-biology/nesoni/metadata.xml| 9 +
sci-biology/nesoni/nesoni-0.117.ebuild | 33 +
3 files changed, 52 insertions(+)
diff --git a/sci-biology/nesoni/ChangeLog b/sci-biology/nesoni/ChangeLog
new file mode 100644
index 000..1e9ab42
--- /dev/null
+++ b/sci-biology/nesoni/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/nesoni
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*nesoni-0.117 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs +metadata.xml,
+ +nesoni-0.117.ebuild:
+ sci-biology/nesoni: new package, needs some dev-lang/R -based packages to be
+ installed
diff --git a/sci-biology/nesoni/metadata.xml b/sci-biology/nesoni/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/nesoni/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/nesoni/nesoni-0.117.ebuild
b/sci-biology/nesoni/nesoni-0.117.ebuild
new file mode 100644
index 000..9f14d79
--- /dev/null
+++ b/sci-biology/nesoni/nesoni-0.117.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Analysis package for next-generation sequencing data and prepare
for IGV display"
+HOMEPAGE="http://www.vicbioinformatics.com/software.nesoni.shtml";
+SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/shrimp
+ sci-biology/bowtie
+ sci-biology/mummer
+ sci-biology/biopython
+ sci-biology/picard
+ dev-lang/R"
+
+ # sci-biology/freebayes
+ # SplitsTree4
+ # BioConductor (limma, edgeR, goseq)
+ # seriation
+ # NMF
[gentoo-commits] proj/sci:master commit in: sci-biology/velvetk/
commit: 6662c1697f2b8a3ca44c0f5e72cdafff5da4d7b8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 09:06:13 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 09:06:13 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6662c169
sci-biology/velvetk: new package
Package-Manager: portage-2.2.7
---
sci-biology/velvetk/ChangeLog | 9 +
sci-biology/velvetk/metadata.xml| 9 +
sci-biology/velvetk/velvetk-20120606.ebuild | 29 +
3 files changed, 47 insertions(+)
diff --git a/sci-biology/velvetk/ChangeLog b/sci-biology/velvetk/ChangeLog
new file mode 100644
index 000..add4df7
--- /dev/null
+++ b/sci-biology/velvetk/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/velvetk
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*velvetk-20120606 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs +metadata.xml,
+ +velvetk-20120606.ebuild:
+ sci-biology/velvetk: new package
diff --git a/sci-biology/velvetk/metadata.xml b/sci-biology/velvetk/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/velvetk/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/velvetk/velvetk-20120606.ebuild
b/sci-biology/velvetk/velvetk-20120606.ebuild
new file mode 100644
index 000..2ebb4f3
--- /dev/null
+++ b/sci-biology/velvetk/velvetk-20120606.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Estimate the best k-mer size to use for your Velvet de novo
assembly"
+HOMEPAGE="http://www.vicbioinformatics.com/software.velvetk.shtml";
+SRC_URI="http://www.vicbioinformatics.com/velvetk.pl";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_prepare(){
+ cp -p "${DISTDIR}"/velvetk.pl . || die
+}
+
+src_install(){
+ dobin velvetk.pl
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
commit: 36271ba96f6900f3219ae9606d6a3757ce21fbd7
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 09:25:33 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 09:25:33 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=36271ba9
sci-biology/VelvetOptimiser: new package
Package-Manager: portage-2.2.7
---
sci-biology/VelvetOptimiser/ChangeLog | 9 +++
.../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 29 ++
sci-biology/VelvetOptimiser/metadata.xml | 9 +++
3 files changed, 47 insertions(+)
diff --git a/sci-biology/VelvetOptimiser/ChangeLog
b/sci-biology/VelvetOptimiser/ChangeLog
new file mode 100644
index 000..573bfac
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/VelvetOptimiser
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*VelvetOptimiser-2.2.5 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs
+ +VelvetOptimiser-2.2.5.ebuild, +metadata.xml:
+ sci-biology/VelvetOptimiser: new package
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
new file mode 100644
index 000..1491603
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Optimise three primary parameter options (K, -exp_cov,
-cov_cutoff) for Velvet sequence assembler."
+HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml";
+SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=sci-biology/bioperl-1.4
+ >=sci-biology/velvet-0.7.5.1
+ >=dev-lang/perl-5.8"
+
+src_install(){
+ dobin VelvetOptimiser.pl
+ insinto ${VENDOR_LIB}/${PN}
+ doins VelvetOpt/*.pm
+ dodoc README INSTALL CHANGELOG || die
+}
diff --git a/sci-biology/VelvetOptimiser/metadata.xml
b/sci-biology/VelvetOptimiser/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
commit: 9cb8f542b9224a22e836a8b6fa6a6b3713adda18
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 09:34:29 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 09:34:29 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cb8f542
sci-biology/VelvetOptimiser: add requirement for threaded perl
Package-Manager: portage-2.2.7
---
sci-biology/VelvetOptimiser/ChangeLog| 4
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/ChangeLog
b/sci-biology/VelvetOptimiser/ChangeLog
index 573bfac..44fa73b 100644
--- a/sci-biology/VelvetOptimiser/ChangeLog
+++ b/sci-biology/VelvetOptimiser/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Apr 2014; Martin Mokrejs
+ VelvetOptimiser-2.2.5.ebuild:
+ sci-biology/VelvetOptimiser: add requirement for threaded perl
+
*VelvetOptimiser-2.2.5 (15 Apr 2014)
15 Apr 2014; Martin Mokrejs
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 1491603..1be9973 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -19,7 +19,7 @@ DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- >=dev-lang/perl-5.8"
+ >=dev-lang/perl-5.8[ithreads]"
src_install(){
dobin VelvetOptimiser.pl
[gentoo-commits] proj/sci:master commit in: sci-biology/bedtools/
commit: 43d38bb3cdfe595def6f13cd1748eda9b1933e27
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Apr 15 21:33:35 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 15 21:33:35 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43d38bb3
sci-biology/bedtools: version bump per bug #505538
Package-Manager: portage-2.2.7
---
sci-biology/bedtools/ChangeLog | 9
sci-biology/bedtools/bedtools-2.19.1.ebuild | 33 +
sci-biology/bedtools/metadata.xml | 16 ++
3 files changed, 58 insertions(+)
diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
new file mode 100644
index 000..530ceb5
--- /dev/null
+++ b/sci-biology/bedtools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/bedtools
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bedtools-2.19.1 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs
+ +bedtools-2.19.1.ebuild, +metadata.xml:
+ sci-biology/bedtools: version bump per bug #505538
diff --git a/sci-biology/bedtools/bedtools-2.19.1.ebuild
b/sci-biology/bedtools/bedtools-2.19.1.ebuild
new file mode 100644
index 000..fd87585
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.19.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header:
/var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.16.2.ebuild,v 1.1
2012/05/29 02:54:40 weaver Exp $
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and
SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/";
+SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/bedtools2-${PV}"
+
+src_prepare() {
+ filter-ldflags -Wl,--as-needed
+ sed -i \
+ -e '/export CXXFLAGS/ d' \
+ -e '/export CXX/ d' \
+ Makefile || die
+}
+
+src_install() {
+ dobin bin/*
+ dodoc README* RELEASE_HISTORY
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/metadata.xml
b/sci-biology/bedtools/metadata.xml
new file mode 100644
index 000..d841c4b
--- /dev/null
+++ b/sci-biology/bedtools/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+ proxy-maintainers
+
+mmokr...@gmail.com
+Martin Mokrejs
+
+
+BEDTools: a flexible suite of utilities for comparing genomic features.
+
+
+bedtools
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/ffindex/
commit: 327968e523bfc4976cf38928a280048b7eb44fc9
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 22:33:25 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 22:33:25 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=327968e5
sci-biology/ffindex: new package, maybe fits better under some other herd?
Package-Manager: portage-2.2.7
---
sci-biology/ffindex/ChangeLog | 9 +++
sci-biology/ffindex/ffindex-0.9.9.3.ebuild | 43 ++
sci-biology/ffindex/metadata.xml | 9 +++
3 files changed, 61 insertions(+)
diff --git a/sci-biology/ffindex/ChangeLog b/sci-biology/ffindex/ChangeLog
new file mode 100644
index 000..a711d80
--- /dev/null
+++ b/sci-biology/ffindex/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ffindex
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ffindex-0.9.9.3 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs
+ +ffindex-0.9.9.3.ebuild, +metadata.xml:
+ sci-biology/ffindex: new package, maybe fits better under some other herd?
diff --git a/sci-biology/ffindex/ffindex-0.9.9.3.ebuild
b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild
new file mode 100644
index 000..1a9a9a1
--- /dev/null
+++ b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Simple index/database for huge amounts of small files"
+HOMEPAGE="http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex";
+SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz";
+
+LICENSE="CC-BY-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/ffindex-0.9.9.3
+
+src_compile(){
+ emake HAVE_MPI=1
+}
+
+src_install(){
+ dodoc README
+ cd src || die
+ dobin ffindex_apply ffindex_unpack ffindex_modify ffindex_get
ffindex_from_fasta ffindex_build ffindex_apply_mpi
+
+ # * QA Notice: The following files contain writable and executable
sections
+ # * Files with such sections will not work properly (or at all!) on
some
+ # * architectures/operating systems. A bug should be filed at
+ # * http://bugs.gentoo.org/ to make sure the issue is fixed.
+ # * For more information, see http://hardened.gentoo.org/gnu-stack.xml
+ # * Please include the following list of files in your report:
+ # * Note: Bugs should be filed for the respective maintainers
+ # * of the package in question and not hardened@g.o.
+ # * RWX --- --- usr/lib64/libffindex.so.0.1
+ #
+ dolib libffindex.so.0.1 libffindex.so
+
+ # make install INSTALL_DIR="${DESTDIR}" HAVE_MPI=1
+}
diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/ffindex/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
commit: 7d88d8fde0145c729b2cf3f147370866db7ed14c
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 22:31:12 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 22:31:12 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d88d8fd
sci-biology/transdecoder: new package
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog | 9 +
sci-biology/transdecoder/metadata.xml | 9 +
.../transdecoder/transdecoder-20140704.ebuild | 44 ++
3 files changed, 62 insertions(+)
diff --git a/sci-biology/transdecoder/ChangeLog
b/sci-biology/transdecoder/ChangeLog
new file mode 100644
index 000..252ef53
--- /dev/null
+++ b/sci-biology/transdecoder/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/transdecoder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*transdecoder-20140704 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs +metadata.xml,
+ +transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: new package
diff --git a/sci-biology/transdecoder/metadata.xml
b/sci-biology/transdecoder/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/transdecoder/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild
b/sci-biology/transdecoder/transdecoder-20140704.ebuild
new file mode 100644
index 000..c539231
--- /dev/null
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
+HOMEPAGE="http://sourceforge.net/projects/transdecoder/";
+SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz";
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+ sci-biology/hmmer
+ sci-biology/cd-hit
+ sci-biology/parafly
+ sci-biology/ffindex"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/TransDecoder_r20140704
+
+src_prepare(){
+ rm -rf 3rd_party
+ mv Makefile Makefile.old
+}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
thread in archives
+#
+# you cna get it from
http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install(){
+ dobin TransDecoder *.pl util/*.pl util/*.sh
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}
+ insinto ${vendor_lib_install_dir}
+ doins PerlLib/*.pm
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/parafly/
commit: aeae301a7d5eba2e10398a056622b6efd6c24654
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 22:34:09 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 22:34:09 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aeae301a
sci-biology/parafly: new package
Package-Manager: portage-2.2.7
---
sci-biology/parafly/ChangeLog | 9 +
sci-biology/parafly/metadata.xml| 9 +
sci-biology/parafly/parafly-20130121.ebuild | 23 +++
3 files changed, 41 insertions(+)
diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog
new file mode 100644
index 000..eb3df3e
--- /dev/null
+++ b/sci-biology/parafly/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/parafly
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*parafly-20130121 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs +metadata.xml,
+ +parafly-20130121.ebuild:
+ sci-biology/parafly: new package
diff --git a/sci-biology/parafly/metadata.xml b/sci-biology/parafly/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/parafly/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/parafly/parafly-20130121.ebuild
b/sci-biology/parafly/parafly-20130121.ebuild
new file mode 100644
index 000..2f9c3ff
--- /dev/null
+++ b/sci-biology/parafly/parafly-20130121.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Some dependency for transdecoder"
+HOMEPAGE="http://sourceforge.net/projects/transdecoder/";
+SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz";
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
+
+src_configure(){
+ ./configure --prefix=/usr
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/RADtools/
commit: 1595e219f373ab70f35f7e7dc96c9aec10518de3
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 22:37:29 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 22:37:29 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1595e219
sci-biology/RADtools: manually install perl modules int PERL5INC path
Package-Manager: portage-2.2.7
---
sci-biology/RADtools/ChangeLog | 6 +-
sci-biology/RADtools/RADtools-1.2.4.ebuild | 8 ++--
sci-biology/RADtools/RADtools-.ebuild | 10 ++
3 files changed, 17 insertions(+), 7 deletions(-)
diff --git a/sci-biology/RADtools/ChangeLog b/sci-biology/RADtools/ChangeLog
index 5896f96..6038117 100644
--- a/sci-biology/RADtools/ChangeLog
+++ b/sci-biology/RADtools/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/RADtools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 08 Jan 2015; Martin Mokrejs
+ RADtools-1.2.4.ebuild, RADtools-.ebuild:
+ sci-biology/RADtools: manually install perl modules int PERL5INC path
+
16 Sep 2014; Christoph Junghans RADtools-1.2.4.ebuild,
RADtools-.ebuild:
removed empty line
diff --git a/sci-biology/RADtools/RADtools-1.2.4.ebuild
b/sci-biology/RADtools/RADtools-1.2.4.ebuild
index 3000e76..5dc2ef3 100644
--- a/sci-biology/RADtools/RADtools-1.2.4.ebuild
+++ b/sci-biology/RADtools/RADtools-1.2.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -32,5 +32,9 @@ RDEPEND="${DEPEND}"
src_install() {
dobin RADMIDs RADmarkers RADpools RADtags
mydoc="CHANGELOG RADmanual.pdf RADmanual.tex README"
- perl-module_src_install DESTDIR="${D}" # install RADtools.pm into @INC
path
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}
+ insinto ${vendor_lib_install_dir}
+ doins *.pm
}
diff --git a/sci-biology/RADtools/RADtools-.ebuild
b/sci-biology/RADtools/RADtools-.ebuild
index 3000e76..44754f5 100644
--- a/sci-biology/RADtools/RADtools-.ebuild
+++ b/sci-biology/RADtools/RADtools-.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
-inherit perl-module
-
[ "$PV" == "" ] && inherit git-2
DESCRIPTION="Tools for processing RAD Sequencing Illumina reads"
@@ -32,5 +30,9 @@ RDEPEND="${DEPEND}"
src_install() {
dobin RADMIDs RADmarkers RADpools RADtags
mydoc="CHANGELOG RADmanual.pdf RADmanual.tex README"
- perl-module_src_install DESTDIR="${D}" # install RADtools.pm into @INC
path
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}
+ insinto ${vendor_lib_install_dir}
+ doins *.pm
}
[gentoo-commits] proj/sci:master commit in: sci-biology/ICC/
commit: 63c8ef5b6d87be51ae5a735c15489dfbdc8bdcf9
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 22:54:21 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 22:54:21 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63c8ef5b
sci-biology/ICC: actually ignore the bundled Parallel module and install it
from portage
---
sci-biology/ICC/ICC-2.0.1.ebuild | 8 +---
1 file changed, 1 insertion(+), 7 deletions(-)
diff --git a/sci-biology/ICC/ICC-2.0.1.ebuild b/sci-biology/ICC/ICC-2.0.1.ebuild
index 5e5fb5c..fe41383 100644
--- a/sci-biology/ICC/ICC-2.0.1.ebuild
+++ b/sci-biology/ICC/ICC-2.0.1.ebuild
@@ -4,8 +4,6 @@
EAPI=5
-inherit perl-module
-
DESCRIPTION="Error corrector for Roche/454 and IonTorrent data with indel and
carryforward, SNP and haplotype calling"
HOMEPAGE="http://indra.mullins.microbiol.washington.edu/ICC";
SRC_URI="http://indra.mullins.microbiol.washington.edu/cgi-bin/ICC/info.cgi?ID=ICC_v2.0.1.zip
-> ICC_v2.0.1.zip"
@@ -16,6 +14,7 @@ KEYWORDS=""
IUSE=""
DEPEND="dev-lang/perl
+ dev-perl/Parallel-ForkManager
sci-biology/ncbi-tools++"
RDEPEND="${DEPEND}"
@@ -24,11 +23,6 @@ S="${WORKDIR}"
src_install(){
dobin Scripts/*.pl
dodoc README.txt
-
- # BUG: does not work
- cd Scripts/lib || die
- perl-module_src_install DESTDIR="${D}" *.pm Parallel/ForkManager.pm #
install into @INC path
-
}
#testing: Blast/Linux/LICENSE OK
[gentoo-commits] proj/sci:master commit in: licenses/
commit: 49de9fa6dab8a54e91794c9a4b72212d271247d4 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jan 8 23:18:13 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jan 8 23:18:13 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=49de9fa6 new license --- licenses/BSD-BroadInstitute | 17 + 1 file changed, 17 insertions(+) diff --git a/licenses/BSD-BroadInstitute b/licenses/BSD-BroadInstitute new file mode 100644 index 000..d9fe246 --- /dev/null +++ b/licenses/BSD-BroadInstitute @@ -0,0 +1,17 @@ +Copyright (c) 2012, The Broad Institute, Inc. All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +· Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + +· Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + +· Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.** + +THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE +BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, +EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +
[gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
commit: 5742accf45fcfa12220b7ff21f6b633f0423ed04
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 15:29:10 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 15:29:10 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5742accf
sci-biology/wcd: version bump, clarify package description, add comments about
addons
Package-Manager: portage-2.2.7
---
sci-biology/wcd/ChangeLog | 10 --
sci-biology/wcd/{wcd-0.6.0.ebuild => wcd-0.6.3.ebuild} | 12 +---
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index be44eea..359dd42 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-biology/wcd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*wcd-0.6.3 (09 Jan 2015)
+
+ 09 Jan 2015; Martin Mokrejs +wcd-0.6.3.ebuild,
+ -wcd-0.6.0.ebuild:
+ sci-biology/wcd: version bump, clarify package description, add comments
about
+ addons
+
03 Mar 2013; Justin Lecher wcd-0.6.0.ebuild,
+files/wcd-0.6.0-impl-decl.patch, +files/wcd-0.6.0-ldflags.patch,
metadata.xml:
@@ -13,4 +20,3 @@
25 Jun 2011; Justin Lecher -wcd-0.6.0_beta.ebuild,
+wcd-0.6.0.ebuild:
Cleaned ebuild
-
diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
similarity index 63%
rename from sci-biology/wcd/wcd-0.6.0.ebuild
rename to sci-biology/wcd/wcd-0.6.3.ebuild
index eb906dc..87c5c51 100644
--- a/sci-biology/wcd/wcd-0.6.0.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -8,9 +8,9 @@ AUTOTOOLS_AUTORECONF=true
inherit autotools-utils flag-o-matic multilib
-DESCRIPTION="Sequence clustering by either of: d2 function, edit distance,
common word heuristics"
+DESCRIPTION="EST sequence clustering by either of: d2 function, edit distance,
common word heuristics"
HOMEPAGE="http://code.google.com/p/wcdest/";
-SRC_URI="http://wcdest.googlecode.com/files/${P}B.tar.gz -> ${P}.tar.gz"
+SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz ->
${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
@@ -43,3 +43,9 @@ src_install() {
use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
autotools-utils_src_install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
}
+
+# consider providing the EMBOSS wrapper for wcd
+#
https://code.google.com/p/wcdest/downloads/detail?name=wcd_emboss_wrap_001.tar.gz
+
+# also consider ESTsim
+#
https://code.google.com/p/wcdest/downloads/detail?name=estsim_distrib.tar.gz&can=2&q=
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
commit: 7e7f17d08f0687cfec7abacfd986c465ca16ee18
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 15:31:02 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 15:31:02 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7e7f17d0
sci-biology/tablet: note the compilation from source is not coded into ebuild
yet
Package-Manager: portage-2.2.7
---
sci-biology/tablet/ChangeLog | 6 +-
sci-biology/tablet/tablet-.ebuild | 4 +++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0cca8d8..7bd423c 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/tablet
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jan 2015; Martin Mokrejs tablet-.ebuild:
+ sci-biology/tablet: note the compilation from source is not coded into ebuild
+ yet
+
*tablet-1.14.04.10 (02 Jul 2014)
02 Jul 2014; Martin Mokrejs
diff --git a/sci-biology/tablet/tablet-.ebuild
b/sci-biology/tablet/tablet-.ebuild
index 1940cb9..7923105 100644
--- a/sci-biology/tablet/tablet-.ebuild
+++ b/sci-biology/tablet/tablet-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -37,6 +37,8 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"
+# TODO: do actually compile tablet from sources
+
src_install() {
java-pkg_dojar lib/tablet-resources.jar || die
java-pkg_dojar lib/tablet.jar || die
[gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/, sci-biology/transdecoder/files/
commit: cf02cac01f101bdcabbd2b3ed95145e97584b925
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 15:34:03 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 15:34:03 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cf02cac0
sci-biology/transdecoder: added patches so that we use PATH to loclate binaries
and not in a local subdirectory named 'util', drop sys-cluster/openmpi
requirement, it does not link against it all all, this is a bunch of perl and
shell scripts
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog | 8 ++
sci-biology/transdecoder/files/TransDecoder.patch | 136 +
.../transdecoder/files/pfam_runner.pl.patch| 20 +++
.../transdecoder/transdecoder-20140704.ebuild | 9 +-
4 files changed, 171 insertions(+), 2 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog
b/sci-biology/transdecoder/ChangeLog
index 252ef53..c564760 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jan 2015; Martin Mokrejs
+ +files/TransDecoder.patch, +files/pfam_runner.pl.patch,
+ transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: added patches so that we use PATH to loclate
+ binaries and not in a local subdirectory named 'util', drop sys-
+ cluster/openmpi requirement, it does not link against it all all, this is a
+ bunch of perl and shell scripts
+
*transdecoder-20140704 (08 Jan 2015)
08 Jan 2015; Martin Mokrejs +metadata.xml,
diff --git a/sci-biology/transdecoder/files/TransDecoder.patch
b/sci-biology/transdecoder/files/TransDecoder.patch
new file mode 100644
index 000..c0cff94
--- /dev/null
+++ b/sci-biology/transdecoder/files/TransDecoder.patch
@@ -0,0 +1,136 @@
+--- /usr/bin/TransDecoder 2015-01-09 11:22:55.0 +0100
TransDecoder 2015-01-09 14:31:44.095839522 +0100
+@@ -48,7 +48,7 @@
+ --prepare_pfam Prepare data for PFAM search and then
quit (for running PFAM on HPC/computing cluster
+ with or without MPI )
+
+- --CPU number of threads to use; (default: 2)
++ --CPU number of threads to use; (default: 1)
+
+ --MPI use MPI w/ execution of hmmscan
+
+@@ -76,7 +76,7 @@
+
+ =head1 PFAM
+
+-You will need hmmer installed. Use hmmpress to prepare the database for hmmer.
++You will need hmmer installed. Use hmmpress from >=hmmer-3.0 to prepare the
database for hmmer.
+ Lhttps://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin>
for downloading the database.
+
+ =head1 CD-HIT
+@@ -105,7 +105,6 @@
+ use Longest_orf;
+
+ my $UTIL_DIR = "$FindBin::RealBin/util";
+-$ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+ $ENV{LD_LIBRARY_PATH} .= ":$FindBin::RealBin/util/lib64";
+
+ my ($cd_hit_est_exec) = &check_program('cd-hit-est');
+@@ -124,7 +123,7 @@
+ my $verbose;
+ my $search_pfam = "";
+ my ($reuse,$pfam_out);
+-my $CPU = 2;
++my $CPU = 1;
+ my $RETAIN_LONG_ORFS = 900;
+ my $MPI = 0;
+
+@@ -330,15 +329,15 @@
+ my $top_cds_file = $train_file && -s $train_file ? $train_file :
"$cds_file.top_${top_ORFs_train}_longest";
+ if (!-s $top_cds_file) {
+ # get longest entries
+-my $cmd = "$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file
$top_ORFs_train > $top_cds_file";
++my $cmd = "get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train >
$top_cds_file";
+
+ unless ($reuse && -s $top_cds_file){
+ if ($cd_hit_est_exec){
+ # to speed things up only check for redundancy up to 4x the
number of entries we want
+ my $red_num = $top_ORFs_train * 4 ;
+-&process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl
$cds_file $red_num > $workdir/redundant_top");
++&process_cmd("get_top_longest_fasta_entries.pl $cds_file $red_num
> $workdir/redundant_top");
+ &process_cmd("$cd_hit_est_exec -r 1 -i $workdir/redundant_top -o
$workdir/redundant_top.nr90 -M 0 -T $CPU >/dev/null 2>/dev/null");
+-&process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl
$workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
++&process_cmd("get_top_longest_fasta_entries.pl
$workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
+ unlink("$workdir/redundant_top");
+ unlink("$workdir/redundant_top.nr90");
+ unlink("$workdir/redundant_top.nr90.bak.clstr");
+@@ -349,20 +348,20 @@
+ }
+ }
[gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
commit: 04e413e188afb955661634805f602e744d3ec5c4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 16:12:34 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 16:12:34 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=04e413e1
sci-biology/ESTate: new package
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 9 +
sci-biology/ESTate/ESTate-0.5.ebuild | 32
sci-biology/ESTate/metadata.xml | 9 +
3 files changed, 50 insertions(+)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
new file mode 100644
index 000..52cfa8c
--- /dev/null
+++ b/sci-biology/ESTate/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ESTate
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ESTate-0.5 (09 Jan 2015)
+
+ 09 Jan 2015; Martin Mokrejs +ESTate-0.5.ebuild,
+ +metadata.xml:
+ sci-biology/ESTate: new package
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild
b/sci-biology/ESTate/ESTate-0.5.ebuild
new file mode 100644
index 000..5b9f468
--- /dev/null
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and
translate)"
+HOMEPAGE="http://www.ebi.ac.uk/~guy/estate";
+SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/estate
+
+src_prepare(){
+ sed -e "s/^CC/#CC/" -e "s/^LDFLAGS/#LDFLAGS/" -e "s/^CFLAGS/#CFLAGS/"
-e "s/LDFLAGS/CFLAGS/" -i src/Makefile || die
+}
+
+src_install(){
+ dobin bin/*
+ doman doc/man/man1/*.1 doc/man/man7/*.7
+ insinto /usr/share/ESTate/etc
+ doins etc/ESTaterc
+ dodoc ANNOUNCE.txt README.txt
+ einfo "Additionally you may want to install sci-biology/wcd which can
be used by ESTate"
+}
diff --git a/sci-biology/ESTate/metadata.xml b/sci-biology/ESTate/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/ESTate/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
commit: 319bfe2c5fe2d5ffc011000547a814696300a8ff
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 17:14:11 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 17:14:11 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=319bfe2c
add the PhD thesis itself as documentation
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 4 +++-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 52cfa8c..6ae928b 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
+ add the PhD thesis itself as documentation
+
*ESTate-0.5 (09 Jan 2015)
09 Jan 2015; Martin Mokrejs +ESTate-0.5.ebuild,
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild
b/sci-biology/ESTate/ESTate-0.5.ebuild
index 5b9f468..989e5f2 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -6,7 +6,8 @@ EAPI=5
DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and
translate)"
HOMEPAGE="http://www.ebi.ac.uk/~guy/estate";
-SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz";
+SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
+ http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz";
LICENSE="GPL-2"
SLOT="0"
@@ -28,5 +29,6 @@ src_install(){
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
dodoc ANNOUNCE.txt README.txt
+ dodoc "${DISTDIR}"/thesis.ps.gz
einfo "Additionally you may want to install sci-biology/wcd which can
be used by ESTate"
}
[gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
commit: 72826ae7fd740933822987a2922daaa22dbb26d8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 17:29:47 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 17:29:47 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=72826ae7
add the probability matrices
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 2 ++
2 files changed, 5 insertions(+)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 6ae928b..628daf7 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
+ add the probability matrices
+
+ 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
add the PhD thesis itself as documentation
*ESTate-0.5 (09 Jan 2015)
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild
b/sci-biology/ESTate/ESTate-0.5.ebuild
index 989e5f2..54704d4 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -28,6 +28,8 @@ src_install(){
doman doc/man/man1/*.1 doc/man/man7/*.7
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
+ doins /usr/share/ESTate/example
+ doins example/embl59* example/drosophila*
dodoc ANNOUNCE.txt README.txt
dodoc "${DISTDIR}"/thesis.ps.gz
einfo "Additionally you may want to install sci-biology/wcd which can
be used by ESTate"
[gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
commit: 74d14fc07ea7c08a447ef8f9d5e14b360f868af2
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 9 17:33:22 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 9 17:33:22 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74d14fc0
use 'insinto' and not 'doins'
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 628daf7..c5cae89 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
+ use 'insinto' and not 'doins'
+
+ 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
add the probability matrices
09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild:
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild
b/sci-biology/ESTate/ESTate-0.5.ebuild
index 54704d4..7fc7970 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -28,7 +28,7 @@ src_install(){
doman doc/man/man1/*.1 doc/man/man7/*.7
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
- doins /usr/share/ESTate/example
+ insinto /usr/share/ESTate/example
doins example/embl59* example/drosophila*
dodoc ANNOUNCE.txt README.txt
dodoc "${DISTDIR}"/thesis.ps.gz
[gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
commit: 1665dd570b59a6962d18316b9e65f672747f1c88 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Jan 9 17:55:46 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Jan 9 17:55:46 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1665dd57 improve description and emphasize the ORF finder can overcome frameshifts in CDS Package-Manager: portage-2.2.7 --- sci-biology/ESTate/ChangeLog | 4 sci-biology/ESTate/ESTate-0.5.ebuild | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog index c5cae89..0e86bdb 100644 --- a/sci-biology/ESTate/ChangeLog +++ b/sci-biology/ESTate/ChangeLog @@ -3,6 +3,10 @@ # $Header: $ 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild: + improve description and emphasize the ORF finder can overcome frameshifts in + CDS + + 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild: use 'insinto' and not 'doins' 09 Jan 2015; Martin Mokrejs ESTate-0.5.ebuild: diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild index 7fc7970..3e459b0 100644 --- a/sci-biology/ESTate/ESTate-0.5.ebuild +++ b/sci-biology/ESTate/ESTate-0.5.ebuild @@ -4,7 +4,7 @@ EAPI=5 -DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and translate)" +DESCRIPTION="ORF finding despite frameshifts, EST clustering (framefinder, estcluster, usage counter, revcomp and translate)" HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"; SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz";
[gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
commit: bd7c62b252cc5351963dafbe3473571d8d1fe1c0
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Jan 10 01:17:40 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Jan 10 01:17:40 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd7c62b2
install *.pm into PERL5LIB/TransDecoder and pass that via env.d
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog| 4
sci-biology/transdecoder/transdecoder-20140704.ebuild | 6 --
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog
b/sci-biology/transdecoder/ChangeLog
index c564760..123bd82 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Martin Mokrejs
+ transdecoder-20140704.ebuild:
+ install *.pm into PERL5LIB/TransDecoder and pass that via env.d
+
09 Jan 2015; Martin Mokrejs
+files/TransDecoder.patch, +files/pfam_runner.pl.patch,
transdecoder-20140704.ebuild:
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild
b/sci-biology/transdecoder/transdecoder-20140704.ebuild
index af5bb4f..c6398f8 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -39,9 +39,11 @@ src_install(){
dobin TransDecoder *.pl util/*.pl util/*.sh
eval `perl '-V:installvendorlib'`
vendor_lib_install_dir="${installvendorlib}"
- dodir ${vendor_lib_install_dir}
- insinto ${vendor_lib_install_dir}
+ dodir ${vendor_lib_install_dir}/TransDecoder
+ insinto ${vendor_lib_install_dir}/TransDecoder
doins PerlLib/*.pm
+ echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" >
${S}"/99TransDecoder"
+ doenvd ${S}"/99TransDecoder" || die
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd
http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin";
[gentoo-commits] proj/sci:master commit in: sci-biology/cegma/
commit: f1305f2410140aee98085c7448eae116695a4b04
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Jan 10 01:20:02 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Jan 10 01:20:02 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1305f24
new package; install *.pm into PERL5LIB/cegma and pass that via env.d
---
sci-biology/cegma/ChangeLog| 8
sci-biology/cegma/cegma-2.5.ebuild | 36
sci-biology/cegma/metadata.xml | 9 +
3 files changed, 53 insertions(+)
diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog
new file mode 100644
index 000..8e87015
--- /dev/null
+++ b/sci-biology/cegma/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/cegma
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 10 Jan 2015; Martin Mokrejs +cegma-2.5.ebuild,
+ +metadata.xml:
+ new package; install *.pm into PERL5LIB/cegma and pass that via env.d
+
diff --git a/sci-biology/cegma/cegma-2.5.ebuild
b/sci-biology/cegma/cegma-2.5.ebuild
new file mode 100644
index 000..ef8dfe5
--- /dev/null
+++ b/sci-biology/cegma/cegma-2.5.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Use set of 458 core proteins to predict genes in a genome and use
them for training to find all genes"
+HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma";
+SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v"${PV}".tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/perl
+ sci-biology/wise
+ >=sci-biology/hmmer-3.0
+ sci-biology/geneid
+ sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/CEGMA_v${PV}
+
+src_install(){
+ dobin bin/*
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}/cegma
+ insinto ${vendor_lib_install_dir}/cegma
+ doins lib/*.pm
+
+ echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma"
+ # echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma"
+ doenvd ${S}"/99cegma" || die
+}
diff --git a/sci-biology/cegma/metadata.xml b/sci-biology/cegma/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/cegma/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/gfftools/
commit: 65b2db85a1e799b5a5c47dd3db55c77e789afb93
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Jan 12 16:43:13 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jan 12 16:43:13 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=65b2db85
sci-biology/gfftools: new package
Package-Manager: portage-2.2.7
---
sci-biology/gfftools/ChangeLog | 9 +
sci-biology/gfftools/gfftools-0.98d.ebuild | 26 ++
sci-biology/gfftools/metadata.xml | 9 +
3 files changed, 44 insertions(+)
diff --git a/sci-biology/gfftools/ChangeLog b/sci-biology/gfftools/ChangeLog
new file mode 100644
index 000..cedf1d5
--- /dev/null
+++ b/sci-biology/gfftools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/gfftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*gfftools-0.98d (12 Jan 2015)
+
+ 12 Jan 2015; Martin Mokrejs
+ +gfftools-0.98d.ebuild, +metadata.xml:
+ sci-biology/gfftools: new package
diff --git a/sci-biology/gfftools/gfftools-0.98d.ebuild
b/sci-biology/gfftools/gfftools-0.98d.ebuild
new file mode 100644
index 000..6cd5cd1
--- /dev/null
+++ b/sci-biology/gfftools/gfftools-0.98d.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="gff2ps can render features annotated in GFF file format into
PostScript figures"
+HOMEPAGE="http://genome.crg.es/software/gfftools/GFF2PS.html";
+SRC_URI="ftp://genome.imim.es/pub/gff_tools/gff2ps/gff2ps_v0.98d.gz
+
http://genome.imim.es/software/gfftools/gff2ps_docs/manual/MANUAL_GFF2PS_v0.96.ps.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+ mv gff2ps_v0.98d gff2ps
+ dobin gff2ps
+ dodoc MANUAL_GFF2PS_v0.96.ps
+}
diff --git a/sci-biology/gfftools/metadata.xml
b/sci-biology/gfftools/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/gfftools/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: /
commit: c992ba97a44bf9870fad6abc92cb029e885fcdec Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Jan 12 16:43:39 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Jan 12 16:43:39 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c992ba97 Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci sci-libs/libfac/ChangeLog | 6 ++- sci-libs/libfac/libfac-3.1.0.ebuild| 10 ++--- sci-libs/libfac/libfac-3.1.1.ebuild| 10 ++--- sci-libs/matio/ChangeLog | 6 ++- sci-libs/matio/matio-1.3.4.ebuild | 32 +++- ...ondor_config-last-rather-than-first-8.3.2.patch | 25 + .../files/condor_config.generic-8.3.2.patch| 43 ++ .../files/condor_shadow_dlopen-8.3.2.patch | 11 ++ ...0.0.patch => packaging_directories-8.3.2.patch} | 6 +-- sys-cluster/htcondor/htcondor-8.3.2.ebuild | 6 +-- 10 files changed, 115 insertions(+), 40 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
commit: 46558c3fddec519dc1b598612c6aadd022dc2aab
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 14 23:25:04 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 14 23:25:04 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=46558c3f
sci-biology/bcftools: new package: compiles against bundled sci-libs/htslib-1.1
but does not install it
Package-Manager: portage-2.2.7
---
sci-biology/bcftools/ChangeLog | 10 ++
sci-biology/bcftools/bcftools-1.1.ebuild | 26 ++
sci-biology/bcftools/metadata.xml| 9 +
3 files changed, 45 insertions(+)
diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
new file mode 100644
index 000..4e0a781
--- /dev/null
+++ b/sci-biology/bcftools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/bcftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bcftools-1.1 (14 Jan 2015)
+
+ 14 Jan 2015; Martin Mokrejs
+ +bcftools-1.1.ebuild, +metadata.xml:
+ sci-biology/bcftools: new package: compiles against bundled sci-
+ libs/htslib-1.1 but does not install it
diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild
b/sci-biology/bcftools/bcftools-1.1.ebuild
new file mode 100644
index 000..e3f446f
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org/bcftools_release_notes";
+SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2";
+
+LICENSE="MIT-GRL"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/htslib
+ dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ sed -e 's#prefix = /usr/local#prefix = /usr#' \
+ -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall
-Wc++-compat -O2@' -i Makefile
+
+ sed -e 's#prefix = /usr/local#prefix = /usr#' \
+ -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall
-Wc++-compat -O2@' -i htslib-1.1/Makefile
+}
diff --git a/sci-biology/bcftools/metadata.xml
b/sci-biology/bcftools/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/bcftools/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/bedtools/
commit: 822634582c5aa77368c8bf6d6b6730d0ee1dd208
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 14 23:36:43 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 14 23:36:43 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=82263458
drop old version which already landed in main tree; add ebuild for new version
Package-Manager: portage-2.2.7
---
sci-biology/bedtools/ChangeLog| 8 +++-
.../bedtools/{bedtools-2.20.1.ebuild => bedtools-2.22.1.ebuild} | 4 ++--
2 files changed, 9 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
index 031b4f9..a36ef57 100644
--- a/sci-biology/bedtools/ChangeLog
+++ b/sci-biology/bedtools/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/bedtools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*bedtools-2.22.1 (14 Jan 2015)
+
+ 14 Jan 2015; Martin Mokrejs
+ +bedtools-2.22.1.ebuild, -bedtools-2.20.1.ebuild:
+ drop old version which already landed in main tree; add ebuild for new
version
+
*bedtools-2.20.1 (30 May 2014)
30 May 2014; Martin Mokrejs
diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild
b/sci-biology/bedtools/bedtools-2.22.1.ebuild
similarity index 91%
rename from sci-biology/bedtools/bedtools-2.20.1.ebuild
rename to sci-biology/bedtools/bedtools-2.22.1.ebuild
index fd87585..877dcad 100644
--- a/sci-biology/bedtools/bedtools-2.20.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header:
/var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.16.2.ebuild,v 1.1
2012/05/29 02:54:40 weaver Exp $
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""
-S="${WORKDIR}/bedtools2-${PV}"
+S="${WORKDIR}/bedtools2"
src_prepare() {
filter-ldflags -Wl,--as-needed
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/, sci-biology/ncbi-blast+/files/
commit: 2cdc6106ceb9e5c89caccfa078a359df07d8ec0c Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 14 23:43:07 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 14 23:43:07 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2cdc6106 sci-biology/ncbi-blast+: new package, ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch --- sci-biology/ncbi-blast+/ChangeLog | 11 + .../files/disable-testsuite-compilation.txt| 3 + sci-biology/ncbi-blast+/files/fix_lib_deps.patch | 668 + sci-biology/ncbi-blast+/metadata.xml | 9 + sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 351 +++ 5 files changed, 1042 insertions(+) diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog new file mode 100644 index 000..819f1f4 --- /dev/null +++ b/sci-biology/ncbi-blast+/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/ncbi-blast+ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*ncbi-blast+-2.2.30 (14 Jan 2015) + + 14 Jan 2015; Martin Mokrejs + +ncbi-blast+-2.2.30.ebuild, +files/disable-testsuite-compilation.txt, + +files/fix_lib_deps.patch, +metadata.xml: + ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch + diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt new file mode 100644 index 000..aeaf75e --- /dev/null +++ b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt @@ -0,0 +1,3 @@ +.* +-.*/test +-.*/unit_test diff --git a/sci-biology/ncbi-blast+/files/fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/fix_lib_deps.patch new file mode 100644 index 000..13dffee --- /dev/null +++ b/sci-biology/ncbi-blast+/files/fix_lib_deps.patch @@ -0,0 +1,668 @@ +Subject: ensure that all libraries link against all direct dependencies + + * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency + loop between libxblast and libxalgoblastdbindex by having the former + provide only the C++ BLAST API, leaving the C core only in libblast. + * src/build-system/library_relations.txt: Change xblast's + relationship to blast from includes to needs, accordingly. + * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect + rather than libconnect for consistency with libblast, which uses the + former to keep the aforementioned cycle-breaking from causing + inconsistency elsewhere. + +Debian-Bug: 633567. +Author: Aaron M. Ucko +Last-Update: 2014-12-02 +--- a/c++/src/algo/blast/core/Makefile.blast.lib b/c++/src/algo/blast/core/Makefile.blast.lib +@@ -21,6 +21,7 @@ LIB = blast + CFLAGS = $(FAST_CFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = composition_adjustment xconnect tables + + WATCHERS = madden camacho + +--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \ + CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi ++ + ASN_DEP = seqset + + WATCHERS = morgulis +--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib b/c++/src/algo/blast/format/Makefile.xblastformat.lib +@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast + + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) + +-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi ++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ ++ seq general xser tables xncbi blastxml2 + + WATCHERS = jianye zaretska madden camacho fongah2 + +--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib b/c++/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + +- ++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi + + USES_LIBRARIES = \ + seqmasks_io +--- a/c++/src/cgi/Makefile.cgi.lib b/c++/src/cgi/Makefile.cgi.lib +@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb + user_agent + LIB = xcgi + ++DLL_LIB = xutil xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov +--- a/c++/src/html/Makefile.html.lib b/c++/src/html/Makefile.html.lib +@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se + commentdiag indentstream html_exception writer_htmlenc + LIB = xhtml + ++DLL_LIB = xncbi ++ + WATCHERS = ivanov + + +--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib b/c++/src/objects/blast/Makefile.xnetblastcli.lib +@@ -3,6 +3,7 @@ ASN_DEP = xnetblast + LIB = xnetblastcli + SRC = blastclient blastclient_ + ++DLL_LIB = xnetblast xser xconnect xutil xncbi + + USES_LIBRARIES = \ + xconnect xnetblast +--
[gentoo-commits] proj/sci:master commit in: /
commit: 5f86af85e0004ac47a3fed36ca1c8c92bd77160a
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 09:55:55 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 09:55:55 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f86af85
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
dev-python/astropy-helpers/ChangeLog | 5 +-
.../astropy-helpers/astropy-helpers-0.4.1.ebuild | 29 +--
dev-python/astropy-helpers/metadata.xml| 4 +-
dev-python/astropy/ChangeLog | 5 +-
licenses/Mendeley-terms| 220 +
sci-libs/arrayfire/arrayfire-.ebuild | 2 +-
sci-libs/dealii/ChangeLog | 8 +-
sci-libs/dealii/Manifest | 2 +
sci-libs/dealii/dealii-8.2.0.ebuild| 2 +-
.../{dealii-.ebuild => dealii-8.2.1.ebuild}| 2 +-
sci-libs/dealii/dealii-.ebuild | 7 +-
sci-libs/libspatialindex/Manifest | 2 +-
.../files/libspatialindex-1.8.1-QA.patch | 15 ++
.../libspatialindex/libspatialindex-1.6.1.ebuild | 19 --
.../libspatialindex/libspatialindex-1.8.5.ebuild | 37
sci-libs/libspatialindex/metadata.xml | 6 +-
sci-misc/kaldi/ChangeLog | 10 +
sci-misc/kaldi/files/Makefile.patch| 19 ++
sci-misc/kaldi/files/configure.patch | 71 +++
sci-misc/kaldi/files/default_rules.mk.patch| 20 ++
sci-misc/kaldi/kaldi-0_p20150101.ebuild| 59 ++
sci-misc/kaldi/metadata.xml| 12 ++
sci-misc/mendeleydesktop/ChangeLog | 14 ++
sci-misc/mendeleydesktop/Manifest | 2 +
.../mendeleydesktop/mendeleydesktop-1.13.1.ebuild | 114 +++
sci-misc/mendeleydesktop/metadata.xml | 9 +
26 files changed, 633 insertions(+), 62 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
commit: 016a54a18482b9ade330b819a0c772a2ff74da8e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 09:54:09 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 09:54:09 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=016a54a1
version bump, masking a crappy package until at least the Makefile's propagate
an error code back to upstream caller,
https://code.google.com/p/mosaik-aligner/issues/detail?id=135
Package-Manager: portage-2.2.7
---
sci-biology/mosaik/ChangeLog | 11 +--
.../mosaik/{mosaik-2.1.33.ebuild => mosaik-2.2.3.ebuild} | 10 --
2 files changed, 17 insertions(+), 4 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 87f4c4b..5116021 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -1,7 +1,15 @@
# ChangeLog for sci-biology/mosaik
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mosaik-2.2.3 (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs
+ +mosaik-2.2.3.ebuild, -mosaik-2.1.33.ebuild:
+ version bump, masking a crappy package until at least the Makefile's
+ propagate an error code back to upstream caller, https://code.google.com/p
+ /mosaik-aligner/issues/detail?id=135
+
07 Jan 2014; Justin Lecher mosaik-2.1.33.ebuild,
mosaik-.ebuild, metadata.xml:
Readd ebuild
@@ -33,4 +41,3 @@
Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266,
Fasta.cpp:268, but the package itself installs and executes at least
mosaik-1.1.0021.ebuild
-
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild
b/sci-biology/mosaik/mosaik-2.2.3.ebuild
similarity index 75%
rename from sci-biology/mosaik/mosaik-2.1.33.ebuild
rename to sci-biology/mosaik/mosaik-2.2.3.ebuild
index bc26a05..6bd994b 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,10 +13,16 @@ SRC_URI="
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+
+# https://code.google.com/p/mosaik-aligner/issues/detail?id=135
S="${WORKDIR}"/MOSAIK-${PV}-source
+src_prepare(){
+ sed -e "s@export LDFLAGS = -Wl@#export LDFLAGS = -Wl@" -i Makefile
+}
+
src_install() {
dobin "${WORKDIR}"/bin/*
[gentoo-commits] proj/sci:master commit in: /
commit: e6ef02c1db4cc08ac7e97754127893aa627cd231
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 11:13:34 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 11:13:34 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e6ef02c1
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
sci-chemistry/nwchem/ChangeLog | 7 +++
.../{nwchem-6.5_p26243-r4.ebuild => nwchem-6.5_p26243-r5.ebuild} | 2 +-
2 files changed, 8 insertions(+), 1 deletion(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/sickle/
commit: a56d140795382c61496629c5048c3ec4fdac87c4 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jan 15 11:13:00 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jan 15 11:13:00 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a56d1407 correct package description Package-Manager: portage-2.2.7 --- sci-biology/sickle/ChangeLog | 6 -- sci-biology/sickle/sickle-.ebuild | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog index bdbc7e7..443ff95 100644 --- a/sci-biology/sickle/ChangeLog +++ b/sci-biology/sickle/ChangeLog @@ -1,11 +1,13 @@ # ChangeLog for sci-biology/sickle -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jan 2015; Martin Mokrejs sickle-.ebuild: + correct package description + *sickle- (24 Mar 2014) 24 Mar 2014; Martin Mokrejs +sickle-.ebuild, +metadata.xml: simple ebuild, bundled Makefile forces compile flags, program version, but works - diff --git a/sci-biology/sickle/sickle-.ebuild b/sci-biology/sickle/sickle-.ebuild index d256d73..022474e 100644 --- a/sci-biology/sickle/sickle-.ebuild +++ b/sci-biology/sickle/sickle-.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 inherit eutils git-r3 -DESCRIPTION="Windowed adaptive adaptor trimming tool for FASTQ data from Illumina/Solexa" +DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa" HOMEPAGE="https://github.com/najoshi/sickle"; EGIT_REPO_URI="https://github.com/najoshi/sickle";
[gentoo-commits] proj/sci:master commit in: sci-biology/sabre/
commit: 0d09d404b268844e465c95d67083f0cce0d1e1e4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 11:44:16 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 11:44:16 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d09d404
sci-biology/sabre: new package
Package-Manager: portage-2.2.7
---
sci-biology/sabre/ChangeLog | 9 +
sci-biology/sabre/metadata.xml | 9 +
sci-biology/sabre/sabre-.ebuild | 39 +
3 files changed, 57 insertions(+)
diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog
new file mode 100644
index 000..f7f747f
--- /dev/null
+++ b/sci-biology/sabre/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/sabre
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*sabre- (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs +metadata.xml,
+ +sabre-.ebuild:
+ sci-biology/sabre: new package
diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/sabre/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/sabre/sabre-.ebuild
b/sci-biology/sabre/sabre-.ebuild
new file mode 100644
index 000..2aee701
--- /dev/null
+++ b/sci-biology/sabre/sabre-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-2
+
+inherit toolchain-funcs
+
+DESCRIPTION="Barcode demultiplexing and trimming tool for Illumina FastQ files"
+HOMEPAGE="https://github.com/najoshi/sabre";
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/najoshi/sabre.git";
+ KEYWORDS=""
+else
+ SRC_URI=""
+ KEYWORDS=""
+fi
+
+
+LICENSE="MIT" # almost verbatim
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+S="${S}"/src
+
+src_prepare(){
+ sed -e "s#OPT = -O3#OPT = ${CFLAGS}#" \
+ -e "s#CC = gcc#CC = $(tc-getCC)#" -i Makefile || die
+}
+
+src_install(){
+ dobin sabre
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/quast/
commit: c0b00572f627ef5eefae26c0c8630b9cef580639
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 11:48:05 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 11:48:05 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c0b00572
version bump
Package-Manager: portage-2.2.7
---
sci-biology/quast/ChangeLog | 8 +++-
sci-biology/quast/{quast-2.2.ebuild => quast-2.3.ebuild} | 2 +-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index ccf3a0e..ed58021 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/quast
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*quast-2.3 (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs +quast-2.3.ebuild,
+ -quast-2.2.ebuild:
+ version bump
+
13 Nov 2014; Justin Lecher quast-2.2.ebuild, metadata.xml:
Bump to new python eclasses
diff --git a/sci-biology/quast/quast-2.2.ebuild
b/sci-biology/quast/quast-2.3.ebuild
similarity index 95%
rename from sci-biology/quast/quast-2.2.ebuild
rename to sci-biology/quast/quast-2.3.ebuild
index 3839147..3cf92e3 100644
--- a/sci-biology/quast/quast-2.2.ebuild
+++ b/sci-biology/quast/quast-2.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
[gentoo-commits] proj/sci:master commit in: sci-biology/quast/
commit: 2bdf22d7d9d5d8553287cf6c324a69a2e4a3226e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 11:51:33 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 11:51:33 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2bdf22d7
added a note about additional bundled package licenses
Package-Manager: portage-2.2.7
---
sci-biology/quast/ChangeLog| 3 +++
sci-biology/quast/quast-2.3.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index ed58021..e29320d 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Jan 2015; Martin Mokrejs quast-2.3.ebuild:
+ added a note about additional bundled package licenses
+
*quast-2.3 (15 Jan 2015)
15 Jan 2015; Martin Mokrejs +quast-2.3.ebuild,
diff --git a/sci-biology/quast/quast-2.3.ebuild
b/sci-biology/quast/quast-2.3.ebuild
index 3cf92e3..701f274 100644
--- a/sci-biology/quast/quast-2.3.ebuild
+++ b/sci-biology/quast/quast-2.3.ebuild
@@ -12,7 +12,7 @@ DESCRIPTION="Compare quality of multiple genome assemblies to
each other"
HOMEPAGE="http://bioinf.spbau.ru/QUAST";
SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz";
-LICENSE="GPL-2"
+LICENSE="GPL-2" # and some other for the bundled copies, see
http://quast.bioinf.spbau.ru/LICENSE
SLOT="0"
KEYWORDS=""
IUSE=""
[gentoo-commits] proj/sci:master commit in: sci-biology/edena/
commit: 3839c43e8d39adf0903e21ecb7da3d92efd48646
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 13:02:54 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 13:02:54 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3839c43e
sci-biology/edena: new package
Package-Manager: portage-2.2.7
---
sci-biology/edena/ChangeLog | 9 +
sci-biology/edena/edena-3.131028.ebuild | 35 +
sci-biology/edena/metadata.xml | 9 +
3 files changed, 53 insertions(+)
diff --git a/sci-biology/edena/ChangeLog b/sci-biology/edena/ChangeLog
new file mode 100644
index 000..a3f0909
--- /dev/null
+++ b/sci-biology/edena/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/edena
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*edena-3.131028 (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs
+ +edena-3.131028.ebuild, +metadata.xml:
+ sci-biology/edena: new package
diff --git a/sci-biology/edena/edena-3.131028.ebuild
b/sci-biology/edena/edena-3.131028.ebuild
new file mode 100644
index 000..0c4fe10
--- /dev/null
+++ b/sci-biology/edena/edena-3.131028.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="De novo short read assembler"
+HOMEPAGE="http://www.genomic.ch/edena.php";
+SRC_URI="http://www.genomic.ch/edena/EdenaV"${PV}".tar.gz";
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/EdenaV"${PV}"
+
+src_prepare(){
+ sed -e "s@^CCC.*@CCC = $(tc-getCXX)@" -e "s@^CFLAGS.*@CFLAGS =
${CFLAGS} -pthread@" -i src/Makefile || die
+}
+
+src_compile(){
+ cd src
+ emake
+}
+
+src_install(){
+ dobin src/edena
+ dodoc referenceManual.pdf
+}
diff --git a/sci-biology/edena/metadata.xml b/sci-biology/edena/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/edena/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/epga/
commit: ac04739d49d0354f0daba854886317a455b798ae
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 15 13:24:36 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 15 13:24:36 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac04739d
sci-biology/epga: new package; no LICENSE file
---
sci-biology/epga/ChangeLog| 10 ++
sci-biology/epga/epga-.ebuild | 36
sci-biology/epga/metadata.xml | 9 +
3 files changed, 55 insertions(+)
diff --git a/sci-biology/epga/ChangeLog b/sci-biology/epga/ChangeLog
new file mode 100644
index 000..5d20948
--- /dev/null
+++ b/sci-biology/epga/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/epga
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*epga- (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs +epga-.ebuild,
+ +metadata.xml:
+ new package; no LICENSE file
+
diff --git a/sci-biology/epga/epga-.ebuild
b/sci-biology/epga/epga-.ebuild
new file mode 100644
index 000..63a50e6
--- /dev/null
+++ b/sci-biology/epga/epga-.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-2
+
+inherit toolchain-funcs
+
+DESCRIPTION="De novo assembler using distribution of reads and insert size"
+HOMEPAGE="https://github.com/bioinfomaticsCSU/EPGA";
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/bioinfomaticsCSU/EPGA.git";
+ KEYWORDS=""
+else
+ SRC_URI=""
+ KEYWORDS=""
+fi
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_compile(){
+ $(tc-getCXX) ${CFLAGS} main.cpp -o epga -lpthread
+}
+
+src_install(){
+ dobin epga
+ dodoc README.md
+}
diff --git a/sci-biology/epga/metadata.xml b/sci-biology/epga/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/epga/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
commit: 43383a65794cbfd08269dbaea69a67d7787479d8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 22 21:45:58 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 22 21:45:58 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43383a65
sci-biology/trimmomatic: new package
Package-Manager: portage-2.2.15
---
sci-biology/trimmomatic/ChangeLog | 9 +++
sci-biology/trimmomatic/metadata.xml| 9 +++
sci-biology/trimmomatic/trimmomatic-0.32.ebuild | 36 +
3 files changed, 54 insertions(+)
diff --git a/sci-biology/trimmomatic/ChangeLog
b/sci-biology/trimmomatic/ChangeLog
new file mode 100644
index 000..119ca3f
--- /dev/null
+++ b/sci-biology/trimmomatic/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/trimmomatic
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*trimmomatic-0.32 (22 Jan 2015)
+
+ 22 Jan 2015; Martin Mokrejs +metadata.xml,
+ +trimmomatic-0.32.ebuild:
+ sci-biology/trimmomatic: new package
diff --git a/sci-biology/trimmomatic/metadata.xml
b/sci-biology/trimmomatic/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/trimmomatic/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
new file mode 100644
index 000..662ceea
--- /dev/null
+++ b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Illumina adapter trimming tool"
+HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic";
+SRC_URI="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
-> "${P}"_manual.pdf"
+
+#
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.6"
+
+# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
+
+EANT_BUILD_TARGET="dist"
+
+src_install() {
+ java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
+ insinto /usr/share/"${PN}"/Illumina
+ doins adapters/*.fa
+ insinto /usr/share/doc/"${P}"
+ dodoc "${DISTDIR}"/"${P}"_manual.pdf
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/geneid/, sci-biology/geneid/files/
commit: e1f1667c293f69f7ae354b3b96fd62b16bc6f141
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jun 17 10:06:04 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jun 17 10:06:04 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1f1667c
sci-biology/geneid: new package, works
Package-Manager: portage-2.2.7
---
sci-biology/geneid/ChangeLog| 9 +
sci-biology/geneid/files/Makefile.patch | 11 +++
sci-biology/geneid/geneid-1.4.4.ebuild | 32
sci-biology/geneid/metadata.xml | 9 +
4 files changed, 61 insertions(+)
diff --git a/sci-biology/geneid/ChangeLog b/sci-biology/geneid/ChangeLog
new file mode 100644
index 000..d140912
--- /dev/null
+++ b/sci-biology/geneid/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/geneid
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*geneid-1.4.4 (17 Jun 2014)
+
+ 17 Jun 2014; Martin Mokrejs
+ +files/Makefile.patch, +geneid-1.4.4.ebuild, +metadata.xml:
+ sci-biology/geneid: new package, works
diff --git a/sci-biology/geneid/files/Makefile.patch
b/sci-biology/geneid/files/Makefile.patch
new file mode 100644
index 000..bd6a866
--- /dev/null
+++ b/sci-biology/geneid/files/Makefile.patch
@@ -0,0 +1,11 @@
+--- geneid/Makefile2014-06-17 11:37:07.0 +0200
geneid/Makefile2014-06-17 11:37:27.0 +0200
+@@ -13,7 +13,7 @@
+ PROGRAM= geneid
+ PRODUCT= $(BIN)/$(PROGRAM)
+ CC=gcc
+-OPTS=-I$(INCLUDE) -Wall -O3
++OPTS=$(CFLAGS) -I$(INCLUDE)
+ #OPTS=-I$(INCLUDE) -Wall -g
+ ###
+
diff --git a/sci-biology/geneid/geneid-1.4.4.ebuild
b/sci-biology/geneid/geneid-1.4.4.ebuild
new file mode 100644
index 000..48bda66
--- /dev/null
+++ b/sci-biology/geneid/geneid-1.4.4.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="An ab initio exon/gene finding program"
+HOMEPAGE="http://genome.crg.es/software/geneid";
+SRC_URI="ftp://genome.crg.es/pub/software/geneid/geneid_v1.4.4.Jan_13_2011.tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${PN}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install() {
+ dobin bin/geneid
+ dohtml docs/*.html
+ dohtml -r docs/chapter*
+ dohtml -r docs/images
+}
diff --git a/sci-biology/geneid/metadata.xml b/sci-biology/geneid/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/geneid/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/sgp2/files/, sci-biology/sgp2/
commit: 12a997ad3dcdf83f8bb23f4d6c0cc87708ebb784
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jun 17 10:42:01 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jun 17 10:42:01 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=12a997ad
sci-biology/sgp2: new package, works
Package-Manager: portage-2.2.7
---
sci-biology/sgp2/ChangeLog| 9
sci-biology/sgp2/files/Makefile.patch | 88 +++
sci-biology/sgp2/metadata.xml | 9
sci-biology/sgp2/sgp2-1.1.ebuild | 34 ++
4 files changed, 140 insertions(+)
diff --git a/sci-biology/sgp2/ChangeLog b/sci-biology/sgp2/ChangeLog
new file mode 100644
index 000..4175f83
--- /dev/null
+++ b/sci-biology/sgp2/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/sgp2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*sgp2-1.1 (17 Jun 2014)
+
+ 17 Jun 2014; Martin Mokrejs
+ +files/Makefile.patch, +metadata.xml, +sgp2-1.1.ebuild:
+ sci-biology/sgp2: new package, works
diff --git a/sci-biology/sgp2/files/Makefile.patch
b/sci-biology/sgp2/files/Makefile.patch
new file mode 100644
index 000..c1d64bd
--- /dev/null
+++ b/sci-biology/sgp2/files/Makefile.patch
@@ -0,0 +1,88 @@
+--- Makefile.ori 2014-06-17 12:24:40.0 +0200
Makefile 2014-06-17 12:26:47.0 +0200
+@@ -39,12 +39,12 @@
+ #
+ ### PATHS
+
+- BBIN = /bin
+- UBIN = /usr/bin
+- LBIN = /usr/local/bin
++ BBIN = $(DESTDIR)/bin
++ UBIN = $(DESTDIR)/usr/bin
++ LBIN = $(DESTDIR)/usr/local/bin
+ #
+ # REMEMBER: INSTALLDIR is the only variable that should be modified
+- INSTALLDIR = $(LBIN)
++ INSTALLDIR = $(UBIN)
+ #
+
+ #
+@@ -97,19 +97,19 @@
+
+SGP2 = sgp2
+ PARSEBLAST = parseblast
+- GENEID = geneid
++# GENEID = geneid
+# HSP2SR = blast2gff
+
+
+- GENEIDD = $(SRC)/geneid
++# GENEIDD = $(SRC)/geneid
+ #HSP2SRD = $(SRC)/blast2gff
+
+- GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \
+- $(wildcard $(addprefix $(GENEIDD)/include/, *.h))
++# GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \
++# $(wildcard $(addprefix $(GENEIDD)/include/, *.h))
+ # HSP2SRSRC = $(wildcard $(addprefix $(HSP2SRD)/src/, *.c)) \
+ # $(wildcard $(addprefix $(HSP2SRD)/include/, *.h))
+
+- SRCCODE = $(GENEID)-sgp $(PARSEBLAST) \
++ SRCCODE = $(PARSEBLAST) \
+$(SGP2)
+ #SRCCODE = $(GENEID)-sgp $(PARSEBLAST) \
+ # $(HSP2SR) $(SGP2)
+@@ -134,9 +134,9 @@
+ cleanbin :
+ -@$(RM) -f $(wildcard $(BIN)/*);
+ rmdir $(BIN);
+- @echo "### Cleaning GENEID..."
+- @cd $(GENEIDD); \
+- $(MAKE) clean;
++# @echo "### Cleaning GENEID..."
++# @cd $(GENEIDD); \
++# $(MAKE) clean;
+ # @echo "### Cleaning HSP2SR..."
+ # @cd $(HSP2SRD); \
+ # $(MAKE) clean;
+@@ -147,6 +147,7 @@
+
+ installbin : $(BINCODE)
+ @echo "### COPYING BIN FILES TO $(INSTALLDIR)...";
++ mkdir -p $(INSTALLDIR);
+ @$(CP) -p $^ $(INSTALLDIR)/;
+
+ #
+@@ -155,14 +156,14 @@
+ $(BIN) :
+ mkdir $(BIN);
+
+-$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID))
+- @${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \
+- $(addprefix $(BIN)/, $(GENEID)-sgp)
+-
+-$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC)
+- @echo "### Making GENEID..."
+- @cd $(GENEIDD); \
+- $(MAKE) -f ./Makefile;
++#$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID))
++# @${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \
++# $(addprefix $(BIN)/, $(GENEID)-sgp)
++
++#$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC)
++# @echo "### Making GENEID..."
++# @cd $(GENEIDD); \
++# $(MAKE) -f ./Makefile;
+
+ #$(addprefix $(BIN)/, $(HSP2SR)) : $(addprefix $(HSP2SRD)/bin/, $(HSP2SR))
+ # @${CP} $(addprefix $(HSP2SRD)/bin/, $(HSP2SR)) \
diff --git a/sci-biology/sgp2/metadata.xml b/sci-biology/sgp2/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/sgp2/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild
new file mode 100644
index 000..cd6becf
--- /dev/null
+++ b/sci-biology/sgp2/sgp2-1.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Find ORFs by comp
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 41e720e3552ebd75742dba2126eeffed95ce6769 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Jun 23 16:17:38 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Jun 23 16:17:38 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=41e720e3 updating the ChangeLog to note where the ncbi-tools++-12.0.0-support-autoconf-2.60.patch comes from --- sci-biology/ncbi-tools++/ChangeLog | 9 - 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 3da37d9..5abfefa 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/ncbi-tools++ -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Jun 2014; Martin Mokrejs ChangeLog: + add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed), + patches from upstream: + http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62745 + http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62750 + http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62760 + 14 Sep 2013; Martin Mokrejs ncbi-tools++-9.0.0-r1.ebuild: Support at least when user passes USE="gnutls -ssl -openssl" but what we
[gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
commit: 1cb6ae89c8b2c693dad53a44dc28c069464a1362
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jun 24 10:47:58 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jun 24 10:47:58 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1cb6ae89
sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps
---
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 37 +++
1 file changed, 37 insertions(+)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
new file mode 100644
index 000..b7b4642
--- /dev/null
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Predict proteins from EST sequences overcoming errors in ORFs"
+HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST";
+SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/emboss
+ sci-biology/estscan
+ sci-biology/bioperl
+ dev-perl/Algorithm-Loops
+ perl-core/File-Path
+ dev-perl/File-Copy
+ perl-core/Getopt-Long
+ dev-perl/Statistics-Descriptive
+ dev-perl/Tie-IxHash"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"p4e3.1b"
+
+src_install(){
+ mydoc="README"
+ perl-module_src_install
+ dobin bin/*.pl
+ dodoc doc/*
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
commit: b6cc46c3c63decdb095aa02234d8aefd8cff81d5 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jun 24 10:48:45 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jun 24 10:48:45 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6cc46c3 sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps --- sci-biology/prot4EST/ChangeLog| 7 +++ sci-biology/prot4EST/metadata.xml | 9 + 2 files changed, 16 insertions(+) diff --git a/sci-biology/prot4EST/ChangeLog b/sci-biology/prot4EST/ChangeLog new file mode 100644 index 000..2469055 --- /dev/null +++ b/sci-biology/prot4EST/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/prot4EST +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 Jun 2014; Martin Mokrejs +metadata.xml: + sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps + diff --git a/sci-biology/prot4EST/metadata.xml b/sci-biology/prot4EST/metadata.xml new file mode 100644 index 000..2bc8930 --- /dev/null +++ b/sci-biology/prot4EST/metadata.xml @@ -0,0 +1,9 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + sci-biology + +mmokr...@fold.natur.cuni.cz +Martin Mokrejs + +
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 3f54d211a74334d29b3c624edc1c96743aa8785b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jun 25 21:02:00 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jun 25 21:02:00 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f54d211
sci-biology/ncbi-tools++-12.0.0: install colliding files under a name suffixed
by a plus sign
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 8 ++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 8ee3f16..6de9b4f 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -339,8 +339,12 @@ src_install() {
# doheader "${S}"_build/inc/*
# File collisions with sci-biology/ncbi-tools
- rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
+ #rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp,vecscreen}
+ mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+ mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+ mv "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+
+ mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
doenvd "${S}/99${PN}"
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 1aca3e5aae88192ca717e47c5a947ef806b69b2e Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jun 25 20:58:36 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jun 25 20:58:36 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1aca3e5a sci-biology/ncbi-tools++-12.0.0: first compile-able ebuild, wow, huge thanks to Aaron Ucko from NCBI developers on the cpp@ mailing list --- .../files/ncbi-tools++-12.0.0-as-needed.patch | 2 +- ...cbi-tools++-12.0.0-linkage-tuneups-addons.patch | 13 + .../ncbi-tools++-12.0.0-linkage-tuneups.patch | 421 + .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild| 14 +- 4 files changed, 444 insertions(+), 6 deletions(-) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch index e97c77f..a9d166e 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch @@ -344,7 +344,7 @@ index 872b92e..78261eb 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb blast xregexp diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib index c7e2778..51ebe9d 100644 --- a/src/algo/phy_tree/Makefile.xalgophytree.lib diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch new file mode 100644 index 000..553e41d --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch @@ -0,0 +1,13 @@ +--- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) +@@ -7,8 +7,8 @@ + SRC = agpconvert + + LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ +-ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) +-LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) ++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch new file mode 100644 index 000..86e96b8 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch @@ -0,0 +1,421 @@ +Index: src/algo/blast/format/Makefile.xblastformat.lib +=== +--- src/algo/blast/format/Makefile.xblastformat.lib(revision 439078) src/algo/blast/format/Makefile.xblastformat.lib(working copy) +@@ -7,6 +7,6 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) + +-DLL_LIB = align_format blastxml xhtml xcgi ++DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi + + WATCHERS = jianye zaretska madden camacho fongah2 +Index: src/app/compart/Makefile.compart.app +=== +--- src/app/compart/Makefile.compart.app (revision 439078) src/app/compart/Makefile.compart.app (working copy) +@@ -5,11 +5,11 @@ + APP = compart + SRC = compart + +-LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ +- $(BLAST_LIBS:%=%$(STATIC)) \ +- $(OBJMGR_LIBS:%=%$(STATIC)) ++LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ ++ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ ++ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) + +-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) +Index: src/app/compart/Makefile.compartp.app +=== +--- src/app/compart/Makefile.compartp.app (revision 439078) src/app/compart/Makefile.compartp.app (working copy) +@@ -5,7 +5,8 @@ + APP = compartp + SRC = compartp + +-LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) ++LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ ++ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + + LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + +Index: src/app/grid/util/Makefile.ncfetch.app +=== +--- src/app/grid/util/Makefile.ncfetch.app (revision 439078) src/app/gri
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: f88f1a0e9b529e9ca95ecec39f080675a4ae20de
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jun 25 23:24:16 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jun 25 23:24:16 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f88f1a0e
sci-biology/ncbi-tools++-12.0.0: dropped unneeded patches, added direct
dependency on glew because the dependency on virtual/opengl does not work
---
.../files/ncbi-tools++-12.0.0-linking.patch| 52 --
.../files/ncbi-tools++-12.0.0-linking2.patch | 10 -
.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild| 7 +--
3 files changed, 2 insertions(+), 67 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
deleted file mode 100644
index 196f3a4..000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
+++ /dev/null
@@ -1,52 +0,0 @@
ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib.ori
(revision 400707)
-+++
ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
(working copy)
-@@ -10,6 +10,6 @@
- LIB_OR_DLL = both
-
- # Dependencies for shared library
--DLL_LIB = ncbi_xreader$(DLL)
-+DLL_LIB = $(GENBANK_LDEP)
-
- WATCHERS = vasilche
ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app.ori (revision
400707)
-+++ ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app (working copy)
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
-
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-
- WATCHERS = kazimird
ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori
(revision 400707)
-+++ ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app
(working copy)
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
-
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
-
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS
ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib.ori
2014-06-24 21:42:11.0 +0200
-+++ ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib2014-06-24
21:42:29.0 +0200
-@@ -10,4 +10,4 @@
-
- WATCHERS = vakatov
-
--DLL_LIB = xncbi xcgi xconnserv xhtml
-+DLL_LIB = xhtml xcgi xconnserv
ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib.ori 2014-06-24
22:54:55.0 +0200
-+++ ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib 2014-06-24
22:55:05.0 +0200
-@@ -8,6 +8,7 @@
- CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
-$(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE
$(ORIG_CPPFLAGS)
-
--DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
-+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) krypto$(DLL) \
-+ kfg$(DLL) kfs$(DLL) klib$(DLL)
-
- LIB_OR_DLL = both
-
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
deleted file mode 100644
index 5507b84..000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
+++ /dev/null
@@ -1,10 +0,0 @@
ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori
2014-06-24 21:50:43.0 +0200
-+++ ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app
2014-06-24 21:50:48.0 +0200
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
-
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
-
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 746a3fe..d8b7d97 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -42,7 +42,7 @@ DEPEND="
mysql? ( virtual/mysql )
ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl )
+ opengl? ( virtual/opengl media-libs/glew )
mesa? ( media-libs/mesa
media-libs/glew
)
@@ -72,7 +72,7 @@ DEPEND="
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
-# seems muParser is required, also glew is required. configure exits otherwise
+# seems muParser is required, also glew is required. configure exits otherwise
if these are explicitly passed to it (due to USE flag enabled)
RDEPEND="${DEPEND}&quo
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 29634acbbe011256ad517af5f0d946c876e7ba12
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 13:29:31 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 13:29:31 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=29634acb
sci-biology/ncbi-tools++-12.0.0: cleanup comments and shutdown a false alarm
message from mv
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index d8b7d97..535b992 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -336,10 +336,9 @@ src_install() {
# doheader "${S}"_build/inc/*
# File collisions with sci-biology/ncbi-tools
- #rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp,vecscreen}
mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
- mv "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+
+ mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop
the eventually mistakenly compiled binaries
mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
[gentoo-commits] proj/sci:master commit in: /
commit: a9e6832d9c8c00bb95a22bb0ae50ef7eb8c91001 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 13:30:00 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 13:30:00 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a9e6832d Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci sci-chemistry/gromacs/ChangeLog | 3 +++ sci-chemistry/gromacs/gromacs-5.0..ebuild | 8 +--- sci-mathematics/Macaulay2/ChangeLog | 3 +++ sci-mathematics/Macaulay2/Macaulay2-.ebuild | 1 + 4 files changed, 8 insertions(+), 7 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
commit: 21729f2ab37071b29b5419db9b6916f65135687d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 13:49:09 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 13:49:09 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21729f2a
sci-biology/barrnap: working ebuild although installing a pre-compiled binary
and until somebody hacks teh main perl code it need to be installed into
/usr/share/{PN} and modifies PATH accordingly
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 15 +++
sci-biology/barrnap/barrnap-0.3.ebuild | 18 ++
2 files changed, 33 insertions(+)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
index df39571..c90ac20 100644
--- a/sci-biology/barrnap/ChangeLog
+++ b/sci-biology/barrnap/ChangeLog
@@ -2,6 +2,21 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 26 Jun 2014; Martin Mokrejs barrnap-0.3.ebuild:
+ sci-biology/barrnap: working ebuild although installing a pre-compiled binary
+ and until somebody hacks teh main perl code it need to be installed into
+ /usr/share/ and modifies
+
/home/mmokrejs/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-
+
gnu/gcc-bin/4.8.2:/opt/vmware/bin:/opt/ucsc-genome-browser/bin:/opt/Apollo:/op
+
t/Tablet:$PATH:/usr/share/cgview_comparison_tool/scripts:/opt/meme/bin:/opt/45
+ 4/bin:/usr/local/pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant-
+ tools/perl:/home/mokrejs/proj/mysql-tools::/usr/local/staden-linux-1-6-0
+
/linux-bin/:/home/mmokrejs/software/i386_linux24/usr/local/bin:/home/mmokrejs/
+
bin/SPDBV:/home/mmokrejs/bin/PDBViewer_230303:/home/mmokrejs/bin/AstexViewer2/
+
bin:/usr/local/modeller9v4/bin:/usr/local/chimera/bin:/opt/454/bin:/usr/local/
+ pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant-
+ tools/perl:/home/mokrejs/proj/mysql-tools: accordingly
+
*barrnap-0.3 (15 Apr 2014)
15 Apr 2014; Martin Mokrejs
+barrnap-0.3.ebuild,
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild
b/sci-biology/barrnap/barrnap-0.3.ebuild
index f5af3ab..68901a7 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -19,4 +19,22 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
+ >=dev-lang/perl-5.6
sci-biology/nesoni"
+
+src_install(){
+ # the below recreates the whole layout
+ insinto /usr/share/"${PN}"
+ doins barrnap
+ chmod a+rx "${D}"/usr/share/"${PN}"/barrnap
+ insinto /usr/share/"${PN}"/binaries
+ doins binaries/nhmmer.linux
+ chmod a+rx "${D}"/usr/share/"${PN}"/binaries/nhmmer.linux
+ insinto /usr/share/"${PN}"/db
+ doins db/*
+ insinto /usr/share/examples
+ doins examples/*
+
+ echo PATH=/usr/share/"${PN}":$PATH > "${S}"/99barrnap
+ doenvd "${S}"/99barrnap
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: a2f461519e3a62831c5d05b9ef0016e9eaf61adc
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 14:31:53 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 14:31:53 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2f46151
sci-biology/ncbi-tools++-12.0.0: dropped altogether openssl-related USE flags
and configure arguments (per upstream info nothing in the public code uses
openssl and the configure test is there for their internal reasonings); dropped
gnutls[lzo] requirement which was only need for unpatched 9.0.0 version;
however, --with-lzo is still advantageous for
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 535b992..f8a3956 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -40,7 +40,6 @@ DEPEND="
sqlite? ( dev-db/sqlite )
sqlite3? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
- ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
mesa? ( media-libs/mesa
@@ -49,7 +48,7 @@ DEPEND="
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
fastcgi? ( www-apache/mod_fastcgi )
- gnutls? ( net-libs/gnutls[lzo] )
+ gnutls? ( net-libs/gnutls )
python? ( dev-lang/python )
cppunit? ( dev-util/cppunit )
icu? ( dev-libs/icu )
@@ -227,7 +226,6 @@ src_configure() {
$(use_with lzo lzo "${EPREFIX}/usr")
$(use_with pcre pcre "${EPREFIX}/usr")
$(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with ssl openssl "${EPREFIX}/usr")
$(use_with ftds ftds "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr")
$(usex fltk --with-fltk="${EPREFIX}/usr" "")
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 4093a5178b56aba0459005460bf7dd5f3d2beba0
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 14:38:00 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 14:38:00 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4093a517
sci-biology/ncbi-tools++-9.0.0*: dropped altogether openssl-related USE flags
and configure arguments (per upstream info nothing in the public code uses
openssl and the configure test is there for their internal reasonings); dropped
gnutls[lzo] requirement which was only need for unpatched 9.0.0 version;
however, --with-lzo is still advantageous for
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html
---
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 8 +++-
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild| 10 ++
2 files changed, 5 insertions(+), 13 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 89ae176..953b011 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -28,7 +28,7 @@ IUSE="
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
- sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+ sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -42,7 +42,6 @@ DEPEND="
sqlite3? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
gnutls? ( net-libs/gnutls )
- ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
mesa? ( media-libs/mesa
@@ -67,7 +66,7 @@ DEPEND="
png? ( media-libs/libpng )
tiff? ( media-libs/tiff )
xpm? ( x11-libs/libXpm )
- dev-libs/lzo
+ lzo? ( dev-libs/lzo )
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
@@ -212,7 +211,7 @@ src_configure() {
# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
-# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc
+# Note: only care about gnutls, nothing actually uses openssl except a
forgotten configure test
$(use_with debug)
$(use_with debug max-debug)
$(use_with debug symbols)
@@ -225,7 +224,6 @@ src_configure() {
$(use_with lzo lzo "${EPREFIX}/usr")
$(use_with pcre pcre "${EPREFIX}/usr")
$(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with ssl openssl "${EPREFIX}/usr")
$(use_with ftds ftds "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr")
$(use_with fltk fltk "${EPREFIX}/usr")
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 8020276..b9f8047 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,7 +23,7 @@ SRC_URI="
LICENSE="public-domain"
SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -36,7 +36,6 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
sqlite3? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )
gnutls? ( net-libs/gnutls )
- ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
mesa? ( media-libs/mesa )
@@ -59,7 +58,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
png? ( media-libs/libpng )
tiff? ( media-libs/tiff )
xpm? ( x11-libs/libXpm )
- dev-libs/lzo
+ lzo? ( dev-libs/lzo )
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
@@ -182,11 +181,6 @@ src_configure() {
else
myconf="--without-gnutls"
fi
- if use ssl; then
- myconf="--with-openssl"
- else
- myconf="--without-openssl"
- fi
if ! use sqlite; then
myconf="--without-sqlite"
fi
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
commit: c9cc902bf22b5154a8dcc82a937da0fd7ebae446 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 15:10:53 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 15:10:53 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c9cc902b sci-biology/ncbi-tools++-12.0.0: added the patch istelf dropping :%=% from LIB settings --- .../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 22 ++ 1 file changed, 22 insertions(+) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch new file mode 100644 index 000..2b94208 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch @@ -0,0 +1,22 @@ +--- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2014-06-26 16:46:27.0 +0200 ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app 2014-06-26 16:47:26.0 +0200 +@@ -9,7 +9,7 @@ + APP = speedtest + SRC = speedtest + LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ +- xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) ++ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + + LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) + +--- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori 2014-06-26 16:47:53.0 +0200 ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app 2014-06-26 16:48:07.0 +0200 +@@ -7,7 +7,7 @@ + + LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ +taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ +- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) ++ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS) + + LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) +
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 47da4cc7e724f425a41f532ce56155fff072657b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 15:09:03 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 15:09:03 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=47da4cc7
sci-biology/ncbi-tools++-12.0.0: dropping :%=% from LIB settings
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index f8a3956..218278d 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -112,6 +112,7 @@ src_prepare() {
"${FILESDIR}"/${P}-more-patches.patch
"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
"${FILESDIR}"/${P}-configure.patch
+ "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
)
# "${FILESDIR}"/${P}-as-needed.patch
# "${FILESDIR}"/${P}-fix-creaders-linking.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
commit: a9c97c981e04e280b2d1b21a54d178f680f0dba4 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 15:52:27 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 15:52:27 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a9c97c98 sci-biology/ncbi-tools++-12.0.0: more entries to ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch --- .../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 22 ++ 1 file changed, 22 insertions(+) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch index 2b94208..44b16ae 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch @@ -19,4 +19,26 @@ + $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS) LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + +--- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori 2014-06-26 17:45:11.0 +0200 ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app 2014-06-26 17:48:26.0 +0200 +@@ -3,7 +3,7 @@ + APP = igblastp + SRC = igblastp_app + LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) +-LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) ++LIB = blast_app_util igblast $(LIB_) + # De-universalize Mac builds to work around a PPC toolchain limitation + CFLAGS = $(FAST_CFLAGS:ppc=i386) +--- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori 2014-06-26 17:47:53.0 +0200 ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app 2014-06-26 17:49:31.0 +0200 +@@ -3,7 +3,7 @@ + APP = igblastn + SRC = igblastn_app + LIB_ = $(BLAST_INPUT_LIBS) xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) +-LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) ++LIB = blast_app_util igblast $(LIB_) + + # De-universalize Mac builds to work around a PPC toolchain limitation + CFLAGS = $(FAST_CFLAGS:ppc=i386)
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
commit: a28e615a1579b782b069ac9f6224c1d24b986788 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 16:56:12 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 16:56:12 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a28e615a sci-biology/ncbi-tools++-12.0.0: more places where to drop ':%=%' --- .../ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch index 44b16ae..fad02c3 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch @@ -16,7 +16,7 @@ LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) -+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS) ++ $(BLAST_LIBS) $(OBJMGR_LIBS) LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: f18aa6a66c0e20b32d49289548aff679a8092be9 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 17:31:01 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 17:31:01 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f18aa6a6 sci-biology/ncbi-tools++-12.0.0: added a blocker with sci-biology/sra_sdk --- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 218278d..cce77ab 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -33,6 +33,7 @@ KEYWORDS="" # sys-libs/db should be compiled with USE=cxx DEPEND=" + !sci-biology/sra_sdk berkdb? ( sys-libs/db:4.3[cxx] ) ftds? ( dev-db/freetds ) boost? ( dev-libs/boost )
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 19b0ba203ab340ea1b4f4ea9f950b3024905127f Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 19:04:06 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 19:04:06 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=19b0ba20 sci-biology/ncbi-tools++-12.0.0: drop forgotten IUSE=ssl --- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index cce77ab..ebc9c33 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -27,7 +27,7 @@ IUSE=" test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" + sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X" #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" KEYWORDS=""
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 2513d463dc99aaf7b5f70f2689f97af7de3c4483
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 19:48:49 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 19:48:49 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2513d463
sci-biology/ncbi-tools++: dropped USE=ftds as it is useless and recommended by
upstream to be disabled altogether
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 14 ++
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 13 ++---
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild| 14 +-
3 files changed, 17 insertions(+), 24 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index ebc9c33..23ff5d8 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -25,8 +25,8 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png
python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
DEPEND="
!sci-biology/sra_sdk
berkdb? ( sys-libs/db:4.3[cxx] )
- ftds? ( dev-db/freetds )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite )
@@ -43,7 +42,7 @@ DEPEND="
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
- mesa? ( media-libs/mesa
+ osmesa? ( media-libs/mesa
media-libs/glew
)
glut? ( media-libs/freeglut )
@@ -70,7 +69,8 @@ DEPEND="
app-arch/bzip2
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
-
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
# seems muParser is required, also glew is required. configure exits otherwise
if these are explicitly passed to it (due to USE flag enabled)
@@ -168,7 +168,6 @@ src_configure() {
#--with-ncbi-public ensure compatibility for all in-house platforms
#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
#--with-sybase-new use newer SYBASE install (12.5 rather than
12.0)
- #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in
FTDS
#--without-spdo not use SP libraries
#--without-orbacus do not use ORBacus CORBA libraries
#--with-orbacus=DIR use ORBacus installation in DIR
@@ -228,11 +227,10 @@ src_configure() {
$(use_with lzo lzo "${EPREFIX}/usr")
$(use_with pcre pcre "${EPREFIX}/usr")
$(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with ftds ftds "${EPREFIX}/usr")
$(use_with mysql mysql "${EPREFIX}/usr")
$(usex fltk --with-fltk="${EPREFIX}/usr" "")
$(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with osmesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 953b011..44c444e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -26,8 +26,8 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
- glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu lzo jpeg osmesa mysql muparser opengl pcre png
python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
# sys-libs/db should be compiled with USE=cxx
DEPEND="
berkdb? ( sys-libs/db:4.3[cxx] )
- ftds? ( dev-db/freetds )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqli
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: d9e17bf2b88b99ee5a31c5406f39cf91964dde10
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 20:41:58 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 20:41:58 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d9e17bf2
sci-biology/ncbi-tools++: fix 'make install if USE=pch
---
.../ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch | 11 +++
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
2 files changed, 12 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
new file mode 100644
index 000..8d53ebe
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori (revision 439078)
ncbi_cxx--12_0_0/src/build-system/Makefile.in.top (working copy)
+@@ -48,7 +48,7 @@
+for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
+cd $(includedir0) && find * -name CVS -prune -o -print |\
+ cpio -pd $(pincludedir)
+- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+
+ install-gbench:
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 23ff5d8..3429e05 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -114,6 +114,7 @@ src_prepare() {
"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
"${FILESDIR}"/${P}-configure.patch
"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
+ "${FILESDIR}"/${P}-fix-install.patch
)
# "${FILESDIR}"/${P}-as-needed.patch
# "${FILESDIR}"/${P}-fix-creaders-linking.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
commit: 5bdca751bc342372b06bcaa65796885de3a1d513 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 20:52:38 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 20:52:38 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5bdca751 sci-biology/ncbi-tools++: reworked patch --- .../ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch | 12 ++-- 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch index 8d53ebe..97e845f 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch @@ -1,11 +1,11 @@ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori (revision 439078) -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top (working copy) +--- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.0 +0200 ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.0 +0200 @@ -48,7 +48,7 @@ -for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done -cd $(includedir0) && find * -name CVS -prune -o -print |\ + for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done + cd $(includedir0) && find * -name CVS -prune -o -print |\ cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) +- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) ++ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) ## set up appropriate build and status directories somewhere under $(libdir)? install-gbench:
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 7d0dda709757bcc413823ffd963152c024551303 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 21:05:51 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 21:05:51 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d0dda70 sci-biology/ncbi-tools++: so require media-libs/mesa[osmesa] for USE=mesa --- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +- sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 2 +- sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild| 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 8280670..d304579 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -42,7 +42,7 @@ DEPEND=" mysql? ( virtual/mysql ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl media-libs/glew ) - mesa? ( media-libs/mesa ) + mesa? ( media-libs/mesa[osmesa] ) glut? ( media-libs/freeglut ) freetype? ( media-libs/freetype ) fastcgi? ( www-apache/mod_fastcgi ) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index e0ca14c..a618abb 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -43,7 +43,7 @@ DEPEND=" gnutls? ( net-libs/gnutls ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) - mesa? ( media-libs/mesa + mesa? ( media-libs/mesa[osmesa] media-libs/glew ) glut? ( media-libs/freeglut ) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild index ab553c5..db91131 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild @@ -37,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 ) gnutls? ( net-libs/gnutls ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) - mesa? ( media-libs/mesa ) + mesa? ( media-libs/mesa[osmesa] ) glut? ( media-libs/freeglut ) freetype? ( media-libs/freetype ) fastcgi? ( www-apache/mod_fastcgi )
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: e5e343c4a4dd2e5df08f92798c800e2ecaf5f4f7 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 26 21:25:35 2014 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 26 21:25:35 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e5e343c4 sci-biology/ncbi-tools++-12.0.0: improved comment text --- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 - 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index d304579..3c28096 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -68,7 +68,10 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge # Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI +# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. +# The default (heavily patched) embedded copy should work, or you can +# leave it off altogether -- the only public apps that make use of it are +# samples and tests, since NCBI's database servers are of course firewalled. # seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 0fc3dc7cd2dabc62b52e5fdba7acc838263e07f4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 26 20:44:53 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 26 20:44:53 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0fc3dc7c
sci-biology/ncbi-tools++: bring back USE=mesa although it is about OSMesa
---
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 8 +++-
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 6 +++---
sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild| 6 +++---
3 files changed, 9 insertions(+), 11 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 3429e05..8280670 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -26,7 +26,7 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png
python
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -42,9 +42,7 @@ DEPEND="
mysql? ( virtual/mysql )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl media-libs/glew )
- osmesa? ( media-libs/mesa
- media-libs/glew
- )
+ mesa? ( media-libs/mesa )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
fastcgi? ( www-apache/mod_fastcgi )
@@ -231,7 +229,7 @@ src_configure() {
$(use_with mysql mysql "${EPREFIX}/usr")
$(usex fltk --with-fltk="${EPREFIX}/usr" "")
$(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with osmesa mesa "${EPREFIX}/usr")
+ $(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 44c444e..e0ca14c 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -27,7 +27,7 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
- glut gnutls hdf5 icu lzo jpeg osmesa mysql muparser opengl pcre png
python
+ glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -43,7 +43,7 @@ DEPEND="
gnutls? ( net-libs/gnutls )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
- osmesa? ( media-libs/osmesa
+ mesa? ( media-libs/mesa
media-libs/glew
)
glut? ( media-libs/freeglut )
@@ -227,7 +227,7 @@ src_configure() {
$(use_with mysql mysql "${EPREFIX}/usr")
$(use_with fltk fltk "${EPREFIX}/usr")
$(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with osmesa mesa "${EPREFIX}/usr")
+ $(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 89b6a96..ab553c5 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,7 +23,7 @@ SRC_URI="
LICENSE="public-domain"
SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut
gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python sablotron
sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut
gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron
sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -37,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
gnutls? ( net-libs/gnutls )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
- osmesa? ( media-libs/mesa )
+ mesa? ( media-libs/mesa )
glut? ( media-libs/freeglut )
[gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
commit: 1d678377b2ad764c6ef12669ca6f9a8e637cf408
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jun 27 07:50:25 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jun 27 07:50:25 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1d678377
sci-biology/VelevtOptimiser: dropping perl version requirement as I am unbale
to check for >=5.8 but make sure 5.16 evaluates as True
---
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 1be9973..55290bc 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -19,7 +19,7 @@ DEPEND=""
RDEPEND="${DEPEND}
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- >=dev-lang/perl-5.8[ithreads]"
+ dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is
recognized as > 5.8, heh
src_install(){
dobin VelvetOptimiser.pl
[gentoo-commits] proj/sci:master commit in: sci-biology/BamView/
commit: 7df8fcb405e9620d5b6ddbd976f41e9521276a28
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jun 27 07:51:10 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jun 27 07:51:10 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7df8fcb4
sci-biology/BamView: fixed java deps
---
sci-biology/BamView/BamView-1.2.11.ebuild | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/BamView/BamView-1.2.11.ebuild
b/sci-biology/BamView/BamView-1.2.11.ebuild
index 44475f4..265fd0e 100644
--- a/sci-biology/BamView/BamView-1.2.11.ebuild
+++ b/sci-biology/BamView/BamView-1.2.11.ebuild
@@ -15,6 +15,7 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="virtual/jdk"
+DEPEND=">=virtual/jdk-1.6
+ dev-java/ant-core"
RDEPEND="${DEPEND}
- virtual/jre"
+ >=virtual/jre-1.6"
[gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
commit: 4af735ef8a1ff95fa9b32415b383c55721d93b90
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jun 27 07:52:06 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jun 27 07:52:06 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4af735ef
sci-biology/prot4EST: remove version numbers from the installed binary filename
---
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index b7b4642..6b4ecf1 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -32,6 +32,7 @@ S="${WORKDIR}"/"p4e3.1b"
src_install(){
mydoc="README"
perl-module_src_install
+ mv bin/prot4EST*.pl bin/prot4EST.pl
dobin bin/*.pl
dodoc doc/*
}
[gentoo-commits] proj/sci:master commit in: sci-biology/ICC/
commit: 7286213decca43e6185a611dc357a71557fd84c9
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 20:39:33 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 20:39:33 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7286213d
sci-biology/ICC: initial ebuild, perl installation steps need to be fixed
---
sci-biology/ICC/ChangeLog| 9 ++
sci-biology/ICC/ICC-2.0.1.ebuild | 61
sci-biology/ICC/metadata.xml | 9 ++
3 files changed, 79 insertions(+)
diff --git a/sci-biology/ICC/ChangeLog b/sci-biology/ICC/ChangeLog
new file mode 100644
index 000..cd415fd
--- /dev/null
+++ b/sci-biology/ICC/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ICC
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ICC-2.0.1 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs +ICC-2.0.1.ebuild:
+ initial ebuild, perl installation steps need to be fixed
+
diff --git a/sci-biology/ICC/ICC-2.0.1.ebuild b/sci-biology/ICC/ICC-2.0.1.ebuild
new file mode 100644
index 000..5e5fb5c
--- /dev/null
+++ b/sci-biology/ICC/ICC-2.0.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Error corrector for Roche/454 and IonTorrent data with indel and
carryforward, SNP and haplotype calling"
+HOMEPAGE="http://indra.mullins.microbiol.washington.edu/ICC";
+SRC_URI="http://indra.mullins.microbiol.washington.edu/cgi-bin/ICC/info.cgi?ID=ICC_v2.0.1.zip
-> ICC_v2.0.1.zip"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+ sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+ dobin Scripts/*.pl
+ dodoc README.txt
+
+ # BUG: does not work
+ cd Scripts/lib || die
+ perl-module_src_install DESTDIR="${D}" *.pm Parallel/ForkManager.pm #
install into @INC path
+
+}
+
+#testing: Blast/Linux/LICENSE OK
+#testing: Example/exampleReads.fas OK
+#testing: Example/exampleReads.qual OK
+#testing: Example/exampleReference.fas OK
+#testing: README.mdOK
+#testing: README.txt OK
+#testing: Scripts/ OK
+#testing: Scripts/CC.plOK
+#testing: Scripts/HIC.pl OK
+#testing: Scripts/IC.plOK
+#testing: Scripts/alignRegion.pl OK
+#testing: Scripts/config.plOK
+#testing: Scripts/lib/ OK
+#testing: Scripts/lib/.DS_StoreOK
+#testing: Scripts/lib/Parallel/OK
+#testing: Scripts/lib/Parallel/ForkManager.pm OK
+#testing: Scripts/lib/paths.pm OK
+#testing: Scripts/lib/seqAlign.pm OK
+#testing: Scripts/lib/utils.pm OK
+#testing: Scripts/ntFreq.plOK
+#testing: Scripts/readQualFilter.pl OK
+#testing: Scripts/retrieveRegion.pl OK
+#testing: Scripts/retrieveWindows.pl OK
+#testing: Scripts/runBLAST.pl OK
+#testing: Scripts/runICC.plOK
+#testing: Scripts/uniqueReads.pl OK
+#testing: VersionHistory.txt OK
+
diff --git a/sci-biology/ICC/metadata.xml b/sci-biology/ICC/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/ICC/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/, sci-biology/bioperl/, sci-biology/jigsaw/, ...
commit: b79af8f82794f511181ab43aa0c20871a4d39723
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 20:42:05 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 20:42:05 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b79af8f8
sci-biology/blue: Initial ebuild, does not install the *.exe.so files. Do we
need them?
---
sci-biology/Atlas/Atlas-2005.ebuild| 18
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 22 +
sci-biology/CAutils/CAutils-20120126.ebuild| 20
sci-biology/InterMine/InterMine-0.98.ebuild| 3 +
sci-biology/MochiView/MochiView-1.45.ebuild| 18
.../ampliconnoise/ampliconnoise-1.27.ebuild| 20
sci-biology/bioperl/bioperl-1.6.901.ebuild | 81
sci-biology/bioperl/metadata.xml | 5 +
sci-biology/blue/ChangeLog | 10 ++
sci-biology/blue/blue-1.1.2.ebuild | 31 ++
sci-biology/blue/metadata.xml | 9 ++
sci-biology/ePCR/ePCR-2.3.12.ebuild| 34 +++
sci-biology/ePCR/files/config.mk.patch | 18
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 +
sci-biology/jigsaw/jigsaw-3.2.10.ebuild| 2 +
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 +
sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild | 22 +
sci-biology/primerD/primerD-1.0.0.ebuild | 3 +
sci-biology/pvmsx/metadata.xml | 9 ++
sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 +
.../tigr-closure/tigr-closure-20080106.ebuild | 66 +
sci-biology/ucsc-genome-browser/metadata.xml | 12 +++
.../ucsc-genome-browser-260.ebuild | 106 +
23 files changed, 606 insertions(+)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild
b/sci-biology/Atlas/Atlas-2005.ebuild
new file mode 100644
index 000..8400820
--- /dev/null
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Atlas Whole Genome Assembly Suite"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite";
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz";
+#
https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
+
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
new file mode 100644
index 000..b918714
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap,
Newbler, Velvet, compare by cross_match"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill";
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# is there an ebuild for newbler?
+DEPEND="dev-lang/perl
+ (sys-cluster/torque || sys/cluster/openpbs)
+ sci-biology/phrap
+ sci-biology/bwa
+ sci-biology/velvet"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild
b/sci-biology/CAutils/CAutils-20120126.ebuild
new file mode 100644
index 000..7b1ca7b
--- /dev/null
+++ b/sci-biology/CAutils/CAutils-20120126.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from
UMD"
+HOMEPAGE="http://www.cbcb.umd.edu/research/CeleraAssembler.shtml";
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-lang/perl"
+
+# is partially included in amos-3.1.0
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild
b/sci-biology/InterMine/InterMine-0.98.ebuild
new file mode 100644
index 000..a06fba7
--- /dev/null
+++ b/sci-biology/InterMine/InterMine-0.98.ebuild
@@ -0,0 +1,3 @@
+http://intermine.org/
+svn co svn://subversion.flymine.org/branches/intermine_0_98
+LGPL-3
diff --git a/sci-biology/MochiView/MochiView-1.45.
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/, sci-biology/InterMine/, sci-biology/ucsc-genome-browser/, ...
commit: 2c54fbea31de3d8b20ca965d780805fdf20dd018
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 20:42:52 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 20:42:52 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c54fbea
Revert "sci-biology/blue: Initial ebuild, does not install the *.exe.so files.
Do we need them?"
This reverts commit b79af8f82794f511181ab43aa0c20871a4d39723.
---
sci-biology/Atlas/Atlas-2005.ebuild| 18
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 22 -
sci-biology/CAutils/CAutils-20120126.ebuild| 20
sci-biology/InterMine/InterMine-0.98.ebuild| 3 -
sci-biology/MochiView/MochiView-1.45.ebuild| 18
.../ampliconnoise/ampliconnoise-1.27.ebuild| 20
sci-biology/bioperl/bioperl-1.6.901.ebuild | 81
sci-biology/bioperl/metadata.xml | 5 -
sci-biology/blue/ChangeLog | 10 --
sci-biology/blue/blue-1.1.2.ebuild | 31 --
sci-biology/blue/metadata.xml | 9 --
sci-biology/ePCR/ePCR-2.3.12.ebuild| 34 ---
sci-biology/ePCR/files/config.mk.patch | 18
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 -
sci-biology/jigsaw/jigsaw-3.2.10.ebuild| 2 -
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 -
sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild | 22 -
sci-biology/primerD/primerD-1.0.0.ebuild | 3 -
sci-biology/pvmsx/metadata.xml | 9 --
sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 -
.../tigr-closure/tigr-closure-20080106.ebuild | 66 -
sci-biology/ucsc-genome-browser/metadata.xml | 12 ---
.../ucsc-genome-browser-260.ebuild | 106 -
23 files changed, 606 deletions(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild
b/sci-biology/Atlas/Atlas-2005.ebuild
deleted file mode 100644
index 8400820..000
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Atlas Whole Genome Assembly Suite"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite";
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz";
-#
https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
deleted file mode 100644
index b918714..000
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap,
Newbler, Velvet, compare by cross_match"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill";
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2";
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# is there an ebuild for newbler?
-DEPEND="dev-lang/perl
- (sys-cluster/torque || sys/cluster/openpbs)
- sci-biology/phrap
- sci-biology/bwa
- sci-biology/velvet"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild
b/sci-biology/CAutils/CAutils-20120126.ebuild
deleted file mode 100644
index 7b1ca7b..000
--- a/sci-biology/CAutils/CAutils-20120126.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from
UMD"
-HOMEPAGE="http://www.cbcb.umd.edu/research/CeleraAssembler.shtml";
-SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz";
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- dev-lang/perl"
-
-# is partially included in amos-3.1.0
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild
b/sci-biology/InterMine/InterMine-0.98.ebuild
deleted file mode 100644
index a06fba7..000
--- a/sci-biology/InterMine/InterMine-0.98.ebuild
+++ /dev/null
@@ -1,3 +0,0 @@
-http://intermine.org/
-svn co svn:/
[gentoo-commits] proj/sci:master commit in: licenses/
commit: 51914e3305d2364a930d6baa6ef7ce2663621c19 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 7 21:35:20 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 7 21:35:20 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=51914e33 update Tablet license --- licenses/Tablet | 38 ++ 1 file changed, 6 insertions(+), 32 deletions(-) diff --git a/licenses/Tablet b/licenses/Tablet index d81931a..296b09c 100644 --- a/licenses/Tablet +++ b/licenses/Tablet @@ -1,36 +1,10 @@ - Tablet uses a modified version of the [1]BSD License which has been - edited to remove references to distribution and use in source forms. - This means that we are happy for you to distribute and use Tablet - however you please, but we do not (yet) want to make the source code - publicly available. +Copyright (c) 2009-2014, Information & Computational Sciences, The James Hutton Institute. +All rights reserved. - The licence and copyright for Tablet is as follows: +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - Copyright © 2009-2013, Information & Computational Sciences, JHI. - All rights reserved. +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - Redistribution and use in binary form, without modification, is - permitted provided that the following conditions are met: +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - - Redistributions must reproduce the above copyright notice, this list - of conditions and the following disclaimer in the documentation and/or - other materials provided with the distribution. - - Neither the name of The James Hutton Institute nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS - IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED - TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A - PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -References - - 1. http://opensource.org/licenses/bsd-license.html +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
[gentoo-commits] proj/sci:master commit in: sci-biology/velvetk/
commit: 2ac683eaf770db8ff97cc6f8c7aa8d2fd5bb7e74
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:39:09 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:39:09 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2ac683ea
added perl to dependencies
Package-Manager: portage-2.2.7
---
sci-biology/velvetk/ChangeLog | 6 +-
sci-biology/velvetk/velvetk-20120606.ebuild | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/velvetk/ChangeLog b/sci-biology/velvetk/ChangeLog
index add4df7..20f03c2 100644
--- a/sci-biology/velvetk/ChangeLog
+++ b/sci-biology/velvetk/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/velvetk
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Jan 2015; Martin Mokrejs
+ velvetk-20120606.ebuild:
+ added perl to dependencies
+
*velvetk-20120606 (15 Apr 2014)
15 Apr 2014; Martin Mokrejs +metadata.xml,
diff --git a/sci-biology/velvetk/velvetk-20120606.ebuild
b/sci-biology/velvetk/velvetk-20120606.ebuild
index 2ebb4f3..b6bfc94 100644
--- a/sci-biology/velvetk/velvetk-20120606.ebuild
+++ b/sci-biology/velvetk/velvetk-20120606.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=""
+DEPEND="dev-lang/perl"
RDEPEND="${DEPEND}"
S="${WORKDIR}"
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: 92575f215ce3ea9efcfa46326947ba00e4676742
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:41:02 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:41:02 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=92575f21
ebuild skeleton
---
sci-biology/primerD/ChangeLog| 10 ++
sci-biology/primerD/metadata.xml | 9 +
sci-biology/primerD/primerD-1.0.0.ebuild | 17 +
3 files changed, 36 insertions(+)
diff --git a/sci-biology/primerD/ChangeLog b/sci-biology/primerD/ChangeLog
new file mode 100644
index 000..f75108a
--- /dev/null
+++ b/sci-biology/primerD/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/primerD
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*primerD-1.0.0 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +primerD-1.0.0.ebuild, +metadata.xml:
+ ebuild skeleton
+
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/primerD/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
new file mode 100644
index 000..21163db
--- /dev/null
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Design degenerate primers"
+HOMEPAGE="http://mblab.wustl.edu/software.html";
+SRC_URI="http://mblab.wustl.edu/software/download/primerD.tar.gz ->
primerD-1.0.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/
commit: a02cb28232bd985520b07b000bd19ae6bc8fb025 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 7 21:42:09 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 7 21:42:09 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a02cb282 added a comment on old version Package-Manager: portage-2.2.7 --- sci-biology/jellyfish/ChangeLog | 6 +- sci-biology/jellyfish/jellyfish-2.1.3.ebuild | 4 +++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog index a5df6d9..cf2f8f7 100644 --- a/sci-biology/jellyfish/ChangeLog +++ b/sci-biology/jellyfish/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/jellyfish -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jan 2015; Martin Mokrejs + jellyfish-2.1.3.ebuild: + added a comment on old version + *jellyfish-2.1.3 (02 Jul 2014) 02 Jul 2014; Martin Mokrejs diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild index 4ac06b2..51f683c 100644 --- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild +++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -9,6 +9,8 @@ HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"; SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"; +# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 + LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86"
[gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
commit: 5c282c71bd4e760c0b99df0188a5ca339bdf8fc9 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 7 21:43:54 2015 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 7 21:43:54 2015 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c282c71 updated checksum types --- sci-biology/est2assembly/metadata.xml | 9 + 1 file changed, 9 insertions(+) diff --git a/sci-biology/est2assembly/metadata.xml b/sci-biology/est2assembly/metadata.xml new file mode 100644 index 000..2bc8930 --- /dev/null +++ b/sci-biology/est2assembly/metadata.xml @@ -0,0 +1,9 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + sci-biology + +mmokr...@fold.natur.cuni.cz +Martin Mokrejs + +
[gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
commit: 1a11e439862e745518e3ac576cfc67dc6f110331
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:43:37 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:43:37 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1a11e439
updated checksum types
---
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 +
sci-biology/est2assembly/est2assembly-.ebuild | 47 +++
2 files changed, 73 insertions(+)
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild
b/sci-biology/est2assembly/est2assembly-1.08.ebuild
new file mode 100644
index 000..72fcd5d
--- /dev/null
+++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
+HOMEPAGE="http://code.google.com/p/est2assembly/";
+SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz";
+
+LICENSE="GPL-v3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-lang/perl
+ app-portage/g-cpan
+ perl-gcpan/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl
+ app-arch/pbzip2"
+RDEPEND="${DEPEND}"
+
diff --git a/sci-biology/est2assembly/est2assembly-.ebuild
b/sci-biology/est2assembly/est2assembly-.ebuild
new file mode 100644
index 000..11284c5
--- /dev/null
+++ b/sci-biology/est2assembly/est2assembly-.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils distutils-r1
+
+[ "$PV" == "" ] && inherit subversion
+
+DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
+HOMEPAGE="http://code.google.com/p/est2assembly/";
+ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk";
+
+if [ "$PV" == "" ]; then
+ ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk";
+ KEYWORDS="~amd64 ~x86"
+else
+
SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_"${PV}".tar.gz";
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+# still missing
+# annot8r http://nematodes.org/bioinformatics/annot8r/index.shtml and
http://nematodes.org/bioinformatics/Annot8r_physprop/
+# prot4EST http://nematodes.org/bioinformatics/prot4EST/
+
+DEPEND="dev-lang/perl
+ dev-perl/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2-bin
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl
+ app-arch/pbzip2"
+RDEPEND="${DEPEND}"
+
+# more install tricks in "${S}"/install.pl
+
+pkg_postinst(){
+ einfo "The package uses mira and newbler assemblers"
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/ePCR/, sci-biology/ePCR/files/
commit: 495d85d8aa9c330e890dfd0102af62b2c3cbf3bf
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:45:36 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:45:36 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=495d85d8
dropped KEYWORDS for incomplete ebuild
---
sci-biology/ePCR/ePCR-2.3.12.ebuild| 34 ++
sci-biology/ePCR/files/config.mk.patch | 18 ++
sci-biology/ePCR/metadata.xml | 9 +
3 files changed, 61 insertions(+)
diff --git a/sci-biology/ePCR/ePCR-2.3.12.ebuild
b/sci-biology/ePCR/ePCR-2.3.12.ebuild
new file mode 100644
index 000..bb82fa3
--- /dev/null
+++ b/sci-biology/ePCR/ePCR-2.3.12.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils
+
+DESCRIPTION="Search for sub-sequences matching PCR primers with correct order,
orientation, and spacing"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/e-pcr/";
+SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-"${PV}"-src.tar.gz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}"/e-PCR-"${PV}
+
+src_prepare(){
+ epatch ${FILESDIR}"/config.mk.patch"
+}
+
+src_compile(){
+ make -j1 srcdir=${S} objdir=${S} || die "make -j1 failed"
+}
+
+src_install(){
+ dobin e-PCR famap fahash re-PCR
+ dodoc README.TXT
+}
diff --git a/sci-biology/ePCR/files/config.mk.patch
b/sci-biology/ePCR/files/config.mk.patch
new file mode 100644
index 000..1960b43
--- /dev/null
+++ b/sci-biology/ePCR/files/config.mk.patch
@@ -0,0 +1,18 @@
+--- stand/config.mk.ori2012-01-16 17:38:11.0 +0100
stand/config.mk2012-01-16 17:39:12.0 +0100
+@@ -52,11 +52,11 @@
+
+ #
+ # GNU compiler flags
+-CC = gcc
+-CXX = g++
+-CXXFLAGS = -I$(srcdir) -I$(INCDIR) $(CC_FLAGS) $(PART_CXXFLAGS) \
++#CC = gcc
++#CXX = g++
++CXXFLAGS = -I$(srcdir) -I$(INCDIR) -I`pwd` \
+ -DDEALLOCATE=0 $(LF64CCFLAGS) $(VERSION_FLAGS) -DSTANDALONE=1
+-LDFLAGS = $(LD_FLAGS) $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) $(PART_LDFLAGS)
++LDFLAGS = $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR)
+ # $(PART_PRELIBS) $(LIBS:%=-l%) $(PART_POSTLIBS)
+
+ LF64CCFLAGS = `getconf LFS_CFLAGS`
diff --git a/sci-biology/ePCR/metadata.xml b/sci-biology/ePCR/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/ePCR/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
commit: 94630596f71351dc8f23722d5fd965fabda645a2
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:46:16 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:46:16 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=94630596
generalized dependency on perl
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 5 -
sci-biology/barrnap/barrnap-0.3.ebuild | 5 +++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
index c90ac20..50bd6cd 100644
--- a/sci-biology/barrnap/ChangeLog
+++ b/sci-biology/barrnap/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/barrnap
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Jan 2015; Martin Mokrejs barrnap-0.3.ebuild:
+ generalized dependency on perl
+
26 Jun 2014; Martin Mokrejs barrnap-0.3.ebuild:
sci-biology/barrnap: working ebuild although installing a pre-compiled binary
and until somebody hacks teh main perl code it need to be installed into
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild
b/sci-biology/barrnap/barrnap-0.3.ebuild
index 68901a7..43d1a13 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -16,10 +16,11 @@ KEYWORDS=""
IUSE=""
# contains bundled binaries of hmmer-3.1 (dev version)
+# needs >=perl-5.6
DEPEND=""
RDEPEND="${DEPEND}
- >=dev-lang/perl-5.6
+ dev-lang/perl
sci-biology/nesoni"
src_install(){
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: 6be36f56d69cd44520a4fb49808511f65e3b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:48:51 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:48:51 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6be36f56
initial ebuild for a new package
Package-Manager: portage-2.2.7
---
sci-biology/ampliconnoise/ChangeLog | 10 ++
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 20
sci-biology/ampliconnoise/metadata.xml | 9 +
3 files changed, 39 insertions(+)
diff --git a/sci-biology/ampliconnoise/ChangeLog
b/sci-biology/ampliconnoise/ChangeLog
new file mode 100644
index 000..eb6ffaa
--- /dev/null
+++ b/sci-biology/ampliconnoise/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/ampliconnoise
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ampliconnoise-1.27 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +ampliconnoise-1.27.ebuild:
+ initial ebuild
+
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
new file mode 100644
index 000..a53392b
--- /dev/null
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Noise removal from pyrosequenced amplicons"
+HOMEPAGE="http://code.google.com/p/ampliconnoise/";
+SRC_URI="http://ampliconnoise.googlecode.com/files/AmpliconNoiseV"${PV}".tar.gz
+ http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
+ http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz";
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
diff --git a/sci-biology/ampliconnoise/metadata.xml
b/sci-biology/ampliconnoise/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/ampliconnoise/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/MochiView/
commit: bbc4afe55941d71c81c170b43cba7ffc467f4508
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:50:01 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:50:01 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bbc4afe5
initial ebuild for a new package
---
sci-biology/MochiView/ChangeLog | 10 ++
sci-biology/MochiView/MochiView-1.45.ebuild | 17 +
sci-biology/MochiView/metadata.xml | 9 +
3 files changed, 36 insertions(+)
diff --git a/sci-biology/MochiView/ChangeLog b/sci-biology/MochiView/ChangeLog
new file mode 100644
index 000..55ef996
--- /dev/null
+++ b/sci-biology/MochiView/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/MochiView
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*MochiView-1.45 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +MochiView-1.45.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/MochiView/MochiView-1.45.ebuild
b/sci-biology/MochiView/MochiView-1.45.ebuild
new file mode 100644
index 000..c1a8145
--- /dev/null
+++ b/sci-biology/MochiView/MochiView-1.45.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Genome browser and analysis"
+HOMEPAGE="http://johnsonlab.ucsf.edu/mochi.html";
+SRC_URI=""
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/MochiView/metadata.xml
b/sci-biology/MochiView/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/MochiView/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/InterMine/
commit: 7c39f140af8d039c1c360699e5e621eccfb549c0
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:52:03 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:52:03 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7c39f140
initial ebuild for a new package
---
sci-biology/InterMine/ChangeLog | 10 ++
sci-biology/InterMine/InterMine-0.98.ebuild | 24
sci-biology/InterMine/metadata.xml | 9 +
3 files changed, 43 insertions(+)
diff --git a/sci-biology/InterMine/ChangeLog b/sci-biology/InterMine/ChangeLog
new file mode 100644
index 000..1c16358
--- /dev/null
+++ b/sci-biology/InterMine/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/InterMine
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*InterMine-0.98 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +InterMine-0.98.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild
b/sci-biology/InterMine/InterMine-0.98.ebuild
new file mode 100644
index 000..f5826c8
--- /dev/null
+++ b/sci-biology/InterMine/InterMine-0.98.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-2
+
+DESCRIPTION="Biological data warehouse integrating complex data"
+HOMEPAGE=""
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/intermine/intermine";
+ KEYWORDS=""
+else
+ SRC_URI=""
+ KEYWORDS=""
+fi
+
+LICENSE="LGPL-v3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/InterMine/metadata.xml
b/sci-biology/InterMine/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/InterMine/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/CAutils/
commit: a33c4998b814ef85373f08d5f92f698a7b5c459e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:53:04 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:53:04 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a33c4998
initial ebuild for a new package
---
sci-biology/CAutils/CAutils-20120126.ebuild | 20
sci-biology/CAutils/metadata.xml| 9 +
2 files changed, 29 insertions(+)
diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild
b/sci-biology/CAutils/CAutils-20120126.ebuild
new file mode 100644
index 000..7b1ca7b
--- /dev/null
+++ b/sci-biology/CAutils/CAutils-20120126.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from
UMD"
+HOMEPAGE="http://www.cbcb.umd.edu/research/CeleraAssembler.shtml";
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-lang/perl"
+
+# is partially included in amos-3.1.0
diff --git a/sci-biology/CAutils/metadata.xml b/sci-biology/CAutils/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/CAutils/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
commit: 8a4f06abb087cbf0c736ab5e9bb53c252e955d1e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:54:27 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:54:27 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a4f06ab
initial ebuild for a new package
---
sci-biology/Atlas/Atlas-2005.ebuild | 18 ++
sci-biology/Atlas/ChangeLog | 10 ++
sci-biology/Atlas/metadata.xml | 9 +
3 files changed, 37 insertions(+)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild
b/sci-biology/Atlas/Atlas-2005.ebuild
new file mode 100644
index 000..29b546d
--- /dev/null
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Atlas Whole Genome Assembly Suite"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite";
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz";
+#
https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas/ChangeLog b/sci-biology/Atlas/ChangeLog
new file mode 100644
index 000..d8bcd83
--- /dev/null
+++ b/sci-biology/Atlas/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas-2005 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs +Atlas-2005.ebuild,
+ +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/Atlas/metadata.xml b/sci-biology/Atlas/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
commit: 13ba695f8aa01b1e62f9a6c0a9f99ce940d9aadc
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 21:58:12 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 21:58:12 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=13ba695f
initial ebuild for a new package
---
sci-biology/pb-honey/metadata.xml| 9 +
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 +
2 files changed, 34 insertions(+)
diff --git a/sci-biology/pb-honey/metadata.xml
b/sci-biology/pb-honey/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/pb-honey/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
new file mode 100644
index 000..c5440bb
--- /dev/null
+++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Structural variant identification (SNV) using long reads (over
10kbp)"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/honey";
+SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/samtools
+ sci-biology/blasr
+ sci-biology/pysam
+ dev-python/h5py
+ dev-python/numpy"
+RDEPEND="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/blue/
commit: 461b242fee3a125f00e7de8fedbf7e20b3392683
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:00:08 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:00:08 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=461b242f
Initial ebuild, does not install the *.exe.so files. Do we need them?
---
sci-biology/blue/ChangeLog | 10 ++
sci-biology/blue/blue-1.1.2.ebuild | 31 +++
sci-biology/blue/metadata.xml | 9 +
3 files changed, 50 insertions(+)
diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
new file mode 100644
index 000..7c74563
--- /dev/null
+++ b/sci-biology/blue/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/blue
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*blue-1.1.2 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs +blue-1.1.2.ebuild,
+ +metadata.xml:
+ Initial ebuild, does not install the *.exe.so files. Do we need them?
+
diff --git a/sci-biology/blue/blue-1.1.2.ebuild
b/sci-biology/blue/blue-1.1.2.ebuild
new file mode 100644
index 000..a4555b3
--- /dev/null
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix
insertions and deletions"
+HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx";
+SRC_URI="http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx
-> "${P}".tar.gz
+
http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx
-> Correcting_reads_with_Blue.pdf"
+
+LICENSE="GPL"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/mono"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/Linux
+
+src_compile(){
+ Blue/compile.sh || die
+ Tessel/compile.sh || die
+ GenerateMerPairs/compile.sh || die
+}
+
+src_install(){
+ dobin Tessel.exe GenerateMerPairs.exe Blue.exe
+ # BUG: probably have to install also the *.exe.so files
+}
diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/blue/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/pb-jelly/
commit: 7f8ffd5d9ba726d2502d2e5d0f4046d6333477ac
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:04:41 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:04:41 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7f8ffd5d
Initial ebuild
---
sci-biology/pb-jelly/ChangeLog | 10 ++
sci-biology/pb-jelly/metadata.xml | 9 +
sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild | 22 ++
3 files changed, 41 insertions(+)
diff --git a/sci-biology/pb-jelly/ChangeLog b/sci-biology/pb-jelly/ChangeLog
new file mode 100644
index 000..7e85562
--- /dev/null
+++ b/sci-biology/pb-jelly/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/pb-jelly
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pb-jelly-14.9.9 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +pb-jelly-14.9.9.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/pb-jelly/metadata.xml
b/sci-biology/pb-jelly/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/pb-jelly/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild
b/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild
new file mode 100644
index 000..78ddcfe
--- /dev/null
+++ b/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Close gaps using PacBio RS or 454 FLX+ reads"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/jelly";
+SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBSuite_14.9.9.tgz ->
pb-jelly-14.9.9.tgz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/blasr
+ <=dev-python/networkx-1.1" # upstream says "Versions past v1.1 have
been shown to have many issues."
+RDEPEND="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/
commit: 3010ecf4051cb4cbab7d5adfceca5bccf1e312df
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:11:27 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:11:27 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3010ecf4
Initial ebuild
---
sci-biology/pvmsx/metadata.xml | 9
sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 ++
2 files changed, 55 insertions(+)
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
new file mode 100644
index 000..07b5255
--- /dev/null
+++ b/sci-biology/pvmsx/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild
b/sci-biology/pvmsx/pvmsx-0.1.ebuild
new file mode 100644
index 000..b194f08
--- /dev/null
+++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR
Gene Indices project tools, an alternative to psx"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/";
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
+
ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz";
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sys-cluster/pvm"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}
+
+src_unpack(){
+ mkdir ${PN} || die
+ cd ${PN} || die "Failed to chdir"
+ unpack ${PN}.tar.gz || die
+}
+
+src_prepare() {
+ # we need gclib from cdbfasta.tar.gz bundle which has fewer files than
tgi_cpp_library.tar.gz wbut has e.g. GStr.h
+ sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT
\${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to
run sed"
+ sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#'
"${S}"/"${PN}"/Makefile || die
+ sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile
+ cd ${PN} || die
+ ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
+}
+
+src_compile() {
+ cd ${PN} || die
+ emake || die "emake failed in "${S}"/${PN}"
+}
+
+src_install() {
+ cd ${PN} || die
+ dobin ${PN} || die "Failed to install ${PN} binary"
+ newdoc README README.${PN}
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/jigsaw/
commit: c987e4deda07df521aebeafc05a5b0c3cb9b751f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:06:34 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:06:34 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c987e4de
Initial ebuild
---
sci-biology/jigsaw/ChangeLog| 10 ++
sci-biology/jigsaw/jigsaw-3.2.10.ebuild | 17 +
sci-biology/jigsaw/metadata.xml | 9 +
3 files changed, 36 insertions(+)
diff --git a/sci-biology/jigsaw/ChangeLog b/sci-biology/jigsaw/ChangeLog
new file mode 100644
index 000..b49b3e1
--- /dev/null
+++ b/sci-biology/jigsaw/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/jigsaw
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jigsaw-3.2.10 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +jigsaw-3.2.10.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
new file mode 100644
index 000..ba8825d
--- /dev/null
+++ b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Combine results from external gene predictors into final gene
models"
+HOMEPAGE="http://www.cbcb.umd.edu/software/jigsaw";
+SRC_URI="http://cbcb.umd.edu/software/jigsaw/"${P}".tar.gz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/jigsaw/metadata.xml b/sci-biology/jigsaw/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/jigsaw/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/tigr-closure/
commit: f7194dde6bb1e013487400d22fa0a663ca909338
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:13:13 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:13:13 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f7194dde
Initial ebuild
---
sci-biology/tigr-closure/ChangeLog | 10
sci-biology/tigr-closure/metadata.xml | 9 +++
.../tigr-closure/tigr-closure-20080106.ebuild | 68 ++
3 files changed, 87 insertions(+)
diff --git a/sci-biology/tigr-closure/ChangeLog
b/sci-biology/tigr-closure/ChangeLog
new file mode 100644
index 000..eba3b60
--- /dev/null
+++ b/sci-biology/tigr-closure/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/tigr-closure
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*tigr-closure-20080106 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +tigr-closure-20080106.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/tigr-closure/metadata.xml
b/sci-biology/tigr-closure/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/tigr-closure/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
new file mode 100644
index 000..068dde9
--- /dev/null
+++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA
sequencing projects"
+HOMEPAGE="http://tigr-closure.sourceforge.net/";
+# http://tigr-closure.svn.sourceforge.net/tigr-closure/
+SRC_URI="tigr-closure-svn-20080106.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_compile() {
+ cd TIGR
+ # install the two *.pm files into our perl path?
+ cd ..
+
+ # Closure Work Order Processing (CWP - CLOVER)
+ # clover and oats
+ cd ${WORKDIR}/CWPSystem/trunk/
+ # needs TIGR/EUIDService.pm in PERL paths
+ make dist
+ # how to install the files from install/ ?
+ cd ../..
+
+ #
+ cd ScaffoldMgmt/trunk
+ make dist
+ # FIXME: unpack the .tar file into image during src_install()
+ cd ../..
+
+ # awfull
+ cd ClosureQC/trunk/
+ mkdir sandbox
+ ${SANDBOX}=${WORKDIR}/sandbox
+ # have ./src/, ./doc, ./install, ./test/work/drivers,
./test/work/getqc, ./test/tmp
+ cd test
+ # ...
+ cd ../../..
+
+ #
+ cd ClosureReactionSystem/trunk
+ make BUILD=true
+ cd ../..
+
+ # some Java servlet?
+ cd AserverConsoleEJB3Hibernate
+ # huh?
+ cd ../..
+}
+
+src_install() {
+ cd ${WORKDIR}/SequenceTiling
+ dobin trunk/src/*.pl
+ cd trunk/src/TIGR/SequenceTiling/
+ myinst="DESTDIR=${D}"
+ perl-module_src_install
+ #
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
commit: 86160d6d6d042a10bd3b1a8b432eaf6db560b6d3
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:24:19 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:24:19 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=86160d6d
Initial ebuild
---
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 23 ++
sci-biology/Atlas_GapFill/ChangeLog| 10 ++
sci-biology/Atlas_GapFill/metadata.xml | 9 +
3 files changed, 42 insertions(+)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
new file mode 100644
index 000..c658019
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap,
Newbler, Velvet, compare by cross_match"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill";
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
+
https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/README
-> ATLAS_GapFill_V2_2.README"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# is there an ebuild for newbler so we could add it to DEPEND?
+DEPEND="dev-lang/perl
+ sys-cluster/torque || ( sys-cluster/openpbs )
+ sci-biology/phrap
+ sci-biology/bwa
+ sci-biology/velvet"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas_GapFill/ChangeLog
b/sci-biology/Atlas_GapFill/ChangeLog
new file mode 100644
index 000..74cc2d8
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas_GapFill
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas_GapFill-2.2 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +Atlas_GapFill-2.2.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/Atlas_GapFill/metadata.xml
b/sci-biology/Atlas_GapFill/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/bioperl/
commit: 66a3f970a48bb2ea70095bbbeab801efd7c617a1
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:27:56 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:27:56 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=66a3f970
bioperl/bioperl-1.6.901: dropped an ebuild with USE=+static, otherwise same in
main tree
---
sci-biology/bioperl/bioperl-1.6.901.ebuild | 81 --
sci-biology/bioperl/metadata.xml | 5 --
2 files changed, 86 deletions(-)
diff --git a/sci-biology/bioperl/bioperl-1.6.901.ebuild
b/sci-biology/bioperl/bioperl-1.6.901.ebuild
deleted file mode 100644
index 98d0763..000
--- a/sci-biology/bioperl/bioperl-1.6.901.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.1.ebuild,v
1.3 2009/10/02 14:51:51 weaver Exp $
-
-EAPI="2"
-
-inherit perl-module
-
-SUBPROJECTS="+db +network +run"
-MIN_PV="1.6"
-
-DESCRIPTION="Perl tools for bioinformatics - Core modules"
-HOMEPAGE="http://www.bioperl.org/";
-# SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2";
-SRC_URI="http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-${PV}.tar.gz";
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
-
-CDEPEND=">=perl-core/Module-Build-0.380.0
- dev-perl/Data-Stag
- dev-perl/libwww-perl
- !minimal? (
- dev-perl/Ace
- dev-perl/Spreadsheet-ParseExcel
- dev-perl/Spreadsheet-WriteExcel
- >=dev-perl/XML-SAX-0.15
- dev-perl/Graph
- dev-perl/SOAP-Lite
- dev-perl/Array-Compare
- dev-perl/SVG
- dev-perl/XML-Simple
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- >=dev-perl/HTML-Parser-3.60
- >=dev-perl/XML-Writer-0.4
- dev-perl/Clone
- dev-perl/XML-DOM
- dev-perl/set-scalar
- dev-perl/XML-XPath
- dev-perl/XML-DOM-XPath
- dev-perl/Algorithm-Munkres
- dev-perl/Data-Stag
- dev-perl/Math-Random
- dev-perl/PostScript
- dev-perl/Convert-Binary-C
- dev-perl/SVG-Graph
- dev-perl/IO-String
- dev-perl/Class-Inspector
- dev-perl/Sort-Naturally
- )
- graphviz? ( dev-perl/GraphViz )
- sqlite? ( dev-perl/DBD-SQLite )"
-DEPEND="virtual/perl-Module-Build
- ${CDEPEND}"
-# In perl-overlay
-# >=virtual/perl-ExtUtils-Manifest-1.52 (to CDEPEND?)
-# >=perl-CPAN/perl-CPAN-1.81
-RDEPEND="${CDEPEND}"
-PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
- db? ( >=sci-biology/bioperl-db-${MIN_PV} )
- network? ( >=sci-biology/bioperl-network-${MIN_PV} )
- run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
-
-S="${WORKDIR}/BioPerl-${PV}"
-
-src_configure() {
- sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
- -e "/'CPAN' *=> *1.81/d" \
- -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" || die
-
- if use minimal && use graphviz; then die "USE flags minimal and
graphviz cannot be used together"; fi
- perl-module_src_configure
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
deleted file mode 100644
index d464821..000
--- a/sci-biology/bioperl/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
- sci-biology
-
[gentoo-commits] proj/sci:master commit in: sci-biology/bioperl/, sci-biology/ucsc-genome-browser/
commit: 06204e7a240e106b481983bdaf48fc4aa9719a4c
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:27:12 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:27:12 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06204e7a
bioperl/bioperl-1.6.901: dropped an ebuild with USE=+static, otherwise same in
main tree
---
sci-biology/bioperl/bioperl-1.6.901.ebuild | 81
sci-biology/bioperl/metadata.xml | 5 +
sci-biology/ucsc-genome-browser/metadata.xml | 12 +++
.../ucsc-genome-browser-260.ebuild | 106 +
4 files changed, 204 insertions(+)
diff --git a/sci-biology/bioperl/bioperl-1.6.901.ebuild
b/sci-biology/bioperl/bioperl-1.6.901.ebuild
new file mode 100644
index 000..98d0763
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.6.901.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.1.ebuild,v
1.3 2009/10/02 14:51:51 weaver Exp $
+
+EAPI="2"
+
+inherit perl-module
+
+SUBPROJECTS="+db +network +run"
+MIN_PV="1.6"
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/";
+# SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2";
+SRC_URI="http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-${PV}.tar.gz";
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
+
+CDEPEND=">=perl-core/Module-Build-0.380.0
+ dev-perl/Data-Stag
+ dev-perl/libwww-perl
+ !minimal? (
+ dev-perl/Ace
+ dev-perl/Spreadsheet-ParseExcel
+ dev-perl/Spreadsheet-WriteExcel
+ >=dev-perl/XML-SAX-0.15
+ dev-perl/Graph
+ dev-perl/SOAP-Lite
+ dev-perl/Array-Compare
+ dev-perl/SVG
+ dev-perl/XML-Simple
+ dev-perl/XML-Parser
+ dev-perl/XML-Twig
+ >=dev-perl/HTML-Parser-3.60
+ >=dev-perl/XML-Writer-0.4
+ dev-perl/Clone
+ dev-perl/XML-DOM
+ dev-perl/set-scalar
+ dev-perl/XML-XPath
+ dev-perl/XML-DOM-XPath
+ dev-perl/Algorithm-Munkres
+ dev-perl/Data-Stag
+ dev-perl/Math-Random
+ dev-perl/PostScript
+ dev-perl/Convert-Binary-C
+ dev-perl/SVG-Graph
+ dev-perl/IO-String
+ dev-perl/Class-Inspector
+ dev-perl/Sort-Naturally
+ )
+ graphviz? ( dev-perl/GraphViz )
+ sqlite? ( dev-perl/DBD-SQLite )"
+DEPEND="virtual/perl-Module-Build
+ ${CDEPEND}"
+# In perl-overlay
+# >=virtual/perl-ExtUtils-Manifest-1.52 (to CDEPEND?)
+# >=perl-CPAN/perl-CPAN-1.81
+RDEPEND="${CDEPEND}"
+PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
+ db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+ network? ( >=sci-biology/bioperl-network-${MIN_PV} )
+ run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+
+S="${WORKDIR}/BioPerl-${PV}"
+
+src_configure() {
+ sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
+ -e "/'CPAN' *=> *1.81/d" \
+ -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" || die
+
+ if use minimal && use graphviz; then die "USE flags minimal and
graphviz cannot be used together"; fi
+ perl-module_src_configure
+}
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
new file mode 100644
index 000..d464821
--- /dev/null
+++ b/sci-biology/bioperl/metadata.xml
@@ -0,0 +1,5 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml
b/sci-biology/ucsc-genome-browser/metadata.xml
new file mode 100644
index 000..18137f6
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+
+ wea...@gentoo.org
+ Andrey Kislyuk
+
+ sci-biology
+
+ Install genome browser Web application. If
this flag is off, only libraries and utilities from the suite are
installed.
+
+
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
n
[gentoo-commits] proj/sci:master commit in: sci-biology/BRANCH/
commit: f16a3ab142fe2668ba1985cdc09c3c0a6f8840c7
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:29:27 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:29:27 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f16a3ab1
Initial ebuild
---
sci-biology/BRANCH/BRANCH-.ebuild | 37 +++
sci-biology/BRANCH/ChangeLog | 10 ++
sci-biology/BRANCH/metadata.xml | 9 +
3 files changed, 56 insertions(+)
diff --git a/sci-biology/BRANCH/BRANCH-.ebuild
b/sci-biology/BRANCH/BRANCH-.ebuild
new file mode 100644
index 000..74be1b1
--- /dev/null
+++ b/sci-biology/BRANCH/BRANCH-.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-2
+
+inherit eutils
+
+DESCRIPTION="Extend partial transcripts with sequence from other reads or
genomic contigs"
+HOMEPAGE=""
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/baoe/BRANCH";
+ KEYWORDS=""
+else
+ SRC_URI=""
+ KEYWORDS=""
+fi
+
+
+LICENSE="Artistic-2"
+SLOT="0"
+IUSE=""
+
+DEPEND="sci-biology/blat
+ sci-libs/lemon"
+RDEPEND="${DEPEND}"
+
+src_compile(){
+ cd BRANCH || die
+ g++ -o BRANCH BRANCH.cpp -lemon -lpthread || die
+}
+
+src_install(){
+ dobin BRANCH/BRANCH
+}
diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog
new file mode 100644
index 000..8954ba6
--- /dev/null
+++ b/sci-biology/BRANCH/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/BRANCH
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*BRANCH- (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +BRANCH-.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/BRANCH/metadata.xml b/sci-biology/BRANCH/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/BRANCH/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
commit: 048f49ddebd47dfe85fdffad7ec869913a6ccec7
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:30:38 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:30:38 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=048f49dd
Initial ebuild
---
sci-biology/SEECER/ChangeLog | 10 ++
sci-biology/SEECER/SEECER-0.1.3.ebuild | 33 +
sci-biology/SEECER/metadata.xml| 9 +
3 files changed, 52 insertions(+)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
new file mode 100644
index 000..1e865a6
--- /dev/null
+++ b/sci-biology/SEECER/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/SEECER
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*SEECER-0.1.3 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +SEECER-0.1.3.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild
b/sci-biology/SEECER/SEECER-0.1.3.ebuild
new file mode 100644
index 000..7f3833e
--- /dev/null
+++ b/sci-biology/SEECER/SEECER-0.1.3.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for RNA-Seq reads"
+HOMEPAGE="http://sb.cs.cmu.edu/seecer/";
+SRC_URI="http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz
+ http://sb.cs.cmu.edu/seecer/downloads/manual.pdf";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-libs/gsl
+ sci-biology/seqan
+ sci-biology/jellyfish"
+RDEPEND="${DEPEND}"
+
+S="${S}"/SEECER
+
+# doh, it install /usr/bin/seecer (note the lowercase letters)
+
+# checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
+#
+# Uses:
+# libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1
(0x7f7853faf000)
+
+
+# dobin bin/run_seecer.sh
+# dodoc "${DISTDIR}"/manual.pdf
diff --git a/sci-biology/SEECER/metadata.xml b/sci-biology/SEECER/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/SEECER/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/trowel/
commit: 0edf409a12707b0fd7acdd5571db00e4db851928
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:33:33 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:33:33 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0edf409a
new, working ebuild
Package-Manager: portage-2.2.7
---
sci-biology/trowel/ChangeLog | 9 +
sci-biology/trowel/metadata.xml | 9 +
sci-biology/trowel/trowel-0.1.4.1.ebuild | 20
3 files changed, 38 insertions(+)
diff --git a/sci-biology/trowel/ChangeLog b/sci-biology/trowel/ChangeLog
new file mode 100644
index 000..a19c10a
--- /dev/null
+++ b/sci-biology/trowel/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/trowel
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*trowel-0.1.4.1 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs +metadata.xml,
+ +trowel-0.1.4.1.ebuild:
+ new, working ebuild
diff --git a/sci-biology/trowel/metadata.xml b/sci-biology/trowel/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/trowel/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/trowel/trowel-0.1.4.1.ebuild
b/sci-biology/trowel/trowel-0.1.4.1.ebuild
new file mode 100644
index 000..c262323
--- /dev/null
+++ b/sci-biology/trowel/trowel-0.1.4.1.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for genomic Illumina FASTQ reads using QUALs and
not coverage info"
+HOMEPAGE="http://sourceforge.net/projects/trowel-ec";
+SRC_URI="http://downloads.sourceforge.net/project/trowel-ec/src/trowel.0.1.4.1.src.tar.gz";
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=dev-libs/boost-1.53.0
+ >=dev-cpp/sparsehash-2.0.2"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/trowel.0.1.4.1.src
[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/
commit: 3348aa6294b4e7ef88327026db0f601c646c95b0
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jan 7 22:42:20 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jan 7 22:42:20 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3348aa62
Initial ebuild
---
sci-biology/trans-abyss/ChangeLog| 10 ++
sci-biology/trans-abyss/metadata.xml | 9 +
sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild | 24
3 files changed, 43 insertions(+)
diff --git a/sci-biology/trans-abyss/ChangeLog
b/sci-biology/trans-abyss/ChangeLog
new file mode 100644
index 000..47ce379
--- /dev/null
+++ b/sci-biology/trans-abyss/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/trans-abyss
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*trans-abyss-1.4.8 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs
+ +trans-abyss-1.4.8.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/trans-abyss/metadata.xml
b/sci-biology/trans-abyss/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/trans-abyss/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
new file mode 100644
index 000..c8538cb
--- /dev/null
+++ b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Analyze and combine multiple assemblies from abyss"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss";
+SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/"${PV}"/trans-ABySS-v"${PV}"_20130916.tar.gz";
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# perl and python
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/trans-ABySS-v"${PV}"
+
+# TODO
+#src_install(){
+#}
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/, sci-biology/vague-bin/files/
commit: 90b414bd2d7195138343e5ea4d129c3e6b067a6e
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jan 8 12:42:22 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 8 12:42:22 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=90b414bd
sci-biology/vague-bin: new java binary package
Package-Manager: portage-2.2.7
---
sci-biology/vague-bin/ChangeLog | 9 ++
sci-biology/vague-bin/files/vague.patch | 8 ++
sci-biology/vague-bin/metadata.xml | 9 ++
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 41
4 files changed, 67 insertions(+)
diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog
new file mode 100644
index 000..30734b2
--- /dev/null
+++ b/sci-biology/vague-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/vague-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vague-bin-1.0.5 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs +files/vague.patch,
+ +metadata.xml, +vague-bin-1.0.5.ebuild:
+ sci-biology/vague-bin: new java binary package
diff --git a/sci-biology/vague-bin/files/vague.patch
b/sci-biology/vague-bin/files/vague.patch
new file mode 100644
index 000..61f4c1a
--- /dev/null
+++ b/sci-biology/vague-bin/files/vague.patch
@@ -0,0 +1,8 @@
+--- vague.ori 2015-01-08 13:31:31.755604378 +0100
vague 2015-01-08 13:31:49.525604424 +0100
+@@ -1,4 +1,4 @@
+ echo "Starting Vague, please wait..."
+ export VAGUE_DIR=`dirname $0`
+ export PATH=$PATH:$VAGUE_DIR
+-java -Xmx3750m -jar `dirname $0`/vague.jar $*
++java -Xmx3750m -jar /usr/share/vague-bin/lib/vague.jar $*
diff --git a/sci-biology/vague-bin/metadata.xml
b/sci-biology/vague-bin/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/vague-bin/metadata.xml
@@ -0,0 +1,9 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+ sci-biology
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
new file mode 100644
index 000..479d88a
--- /dev/null
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+[ "$PV" == "" ] && inherit git-2
+
+DESCRIPTION="GUI for Velvet de novo assembler"
+HOMEPAGE="http://www.vicbioinformatics.com/software.vague.shtml";
+
+if [ "$PV" == "" ]; then
+
EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague";
+ KEYWORDS=""
+else
+ SRC_URI="http://www.vicbioinformatics.com/vague-"${PV}".tar.gz";
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jre-1.5
+ sci-biology/velvet
+ sci-biology/velvetk"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/vague-"${PV}"
+
+src_prepare(){
+ epatch "${FILESDIR}"/vague.patch
+}
+
+src_install(){
+ dobin vague
+ java-pkg_dojar vague.jar || die
+}
