commit: 2dffd7378f16086d11d32432d30d0325d40d3238
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 18:53:23 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 18:53:23 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2dffd737
sci-biology/trinityrnaseq: version bump (no KEYWORDS set)
The perl include paths are not matching the paths in *.pm files
all *.pm need to be patched so that they could be placed into
site_perl subdirectory.
In brief, the package still does not support installation into
a site-wide directory. users are supposed to executed off the
unpacked tarball directly.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
...trinityrnaseq-2.1.1-disable_some_plugins.patch} | 0
.../trinityrnaseq-2.6.6-disable_some_plugins.patch | 23 ++++++++++
.../trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 4 +-
.../trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 4 +-
.../trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 4 +-
...seq-2.1.1.ebuild => trinityrnaseq-2.6.6.ebuild} | 53 +++++++++++-----------
6 files changed, 56 insertions(+), 32 deletions(-)
diff --git a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch
b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
similarity index 100%
rename from sci-biology/trinityrnaseq/files/disable_some_plugins.patch
rename to
sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
diff --git
a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
new file mode 100644
index 000000000..02f4d5d8a
--- /dev/null
+++
b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
@@ -0,0 +1,23 @@
+--- trinity-plugins/Makefile 2018-04-21 20:01:58.389880915 +0200
++++ trinity-plugins/Makefile 2018-04-21 20:03:31.752684954 +0200
+@@ -7,7 +7,7 @@
+
+
+
+-trinity_essentials: seqtk_target parafly_target trimmomatic_target
++trinity_essentials: parafly_target
+
+ trimmomatic_target:
+ ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+@@ -39,11 +39,9 @@
+ cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf
${COLLECTL_CODE} collectl
+
+ clean:
+- rm -rf ./seqtk-trinity-0.0.2
+ cd scaffold_iworm_contigs && $(MAKE) clean
+ cd parafly-code && $(MAKE) clean
+ rm -f ./parafly # rm symlink
+- rm -f ./Trimmomatic # rm symlink
+ cd slclust && $(MAKE) clean
+ cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
+ @echo "\n\n** Done cleaning plugins area **"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 95a9ae58d..1941db22a 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -21,7 +21,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
sci-biology/samtools:0.1-legacy
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 952d3a41a..8f131cb17 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -20,7 +20,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index a6692a0ec..19085d752 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -20,7 +20,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
similarity index 52%
copy from sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
copy to sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
index 952d3a41a..238766eed 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -10,33 +10,34 @@ inherit perl-module eutils toolchain-funcs
DESCRIPTION="Transcriptome assembler for RNA-seq reads"
HOMEPAGE="http://trinityrnaseq.github.io/";
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz
-> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.2.6:2
>=sci-libs/htslib-1.2.1
- sci-biology/samtools:0.1-legacy
- >=sci-biology/trimmomatic-0.32
+ >=sci-biology/samtools-1.3:0
+ >=sci-biology/trimmomatic-0.36
>=sci-biology/GAL-0.2.1
- dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
+ dev-perl/IO-All
+ sci-biology/seqtools"
# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
+# has the following "plugins" (aka bundled 3rd-party code)
+# slclust
+# DEXseq_util
+# COLLECTL
+# ParaFly-0.1.0
+
+S="${WORKDIR}"/trinityrnaseq-Trinity-v"${PV}"
src_prepare(){
- epatch "${FILESDIR}"/disable_some_plugins.patch
+ epatch "${FILESDIR}"/"${P}"-disable_some_plugins.patch
}
#src_compile(){
@@ -45,19 +46,21 @@ src_prepare(){
#}
src_install(){
+ dodoc Chrysalis/chrysalis.notes
+ dodoc Changelog.txt
perl_set_version
dobin Trinity util/*.pl
- # should become a new package depending on dev-perl/IO-All
- dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
- dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
- #
- insinto /usr/share/"${PN}"/util
- rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
- doins -r util/*
- #
dobin Inchworm/bin/*
cd Chrysalis || die
- dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta
IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly
TranscriptomeFromVaryK analysis/ReadsToComponents.pl
+ dobin MakeDepend checkLock BreakTransByPairs BubbleUpClustering
Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI
IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts
ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly
TranscriptomeFromVaryK analysis/ReadsToComponents.pl
+ cd ../util/R || die
+ insinto /usr/share/"${PN}"/R
+ doins *.R
+ cd ../PBS || die
+ insinto /usr/share/"${PN}"/PBS
+ doins *
+ cd .. || die
+ cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
cd "${S}" || die
insinto "${VENDOR_LIB}/${PN}"
doins util/misc/PerlLib/*.pm PerlLib/*.pm
@@ -65,8 +68,6 @@ src_install(){
doins PerlLib/KmerGraphLib/*.pm
insinto "${VENDOR_LIB}/${PN}"/CDNA
doins PerlLib/CDNA/*.pm
- insinto "${VENDOR_LIB}/${PN}"/HPC
- doins PerlLib/HPC/*.pm
insinto "${VENDOR_LIB}/${PN}"/Simulate
doins PerlLib/Simulate/*.pm
insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
