commit: e99e0ca02a5335c1528d004692a2ca3610165cdd Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sun Oct 26 16:15:19 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Oct 26 16:15:19 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e99e0ca0
Moved to tree Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> --- sci-biology/consed/ChangeLog | 41 ----------- sci-biology/consed/consed-20-r1.ebuild | 80 ---------------------- sci-biology/consed/consed-21.ebuild | 80 ---------------------- sci-biology/consed/consed-22.ebuild | 80 ---------------------- sci-biology/consed/consed-23.ebuild | 80 ---------------------- sci-biology/consed/consed-24.ebuild | 80 ---------------------- sci-biology/consed/consed-25.ebuild | 80 ---------------------- sci-biology/consed/consed-26.ebuild | 80 ---------------------- sci-biology/consed/consed-27.ebuild | 80 ---------------------- sci-biology/consed/files/nLine.h.patch | 17 ----- .../consed/files/nextPhredPipeline.cpp.patch | 11 --- sci-biology/consed/metadata.xml | 9 --- 12 files changed, 718 deletions(-) diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog deleted file mode 100644 index 4bbf7b9..0000000 --- a/sci-biology/consed/ChangeLog +++ /dev/null @@ -1,41 +0,0 @@ -# ChangeLog for sci-biology/consed -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 05 Apr 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> 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 <mmokr...@fold.natur.cuni.cz> 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 <mmokr...@fold.natur.cuni.cz> 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: replace hardcoded CONSED_HOME path in installed perl - scripts to fix situations when user has for some reason an empty CONSED_HOME - -*consed-27 (23 Mar 2014) -*consed-26 (23 Mar 2014) -*consed-25 (23 Mar 2014) -*consed-24 (23 Mar 2014) -*consed-23 (23 Mar 2014) -*consed-22 (23 Mar 2014) -*consed-21 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> - consed-20-r1.ebuild, +consed-21.ebuild, +consed-22.ebuild, - files/nLine.h.patch, files/nextPhredPipeline.cpp.patch, metadata.xml: - Added versions 21, 22, 23, 24, 25, 26, 27. None of them need the two - patches anymore but all of them need samtools for BAM support. - Compiled with x86_64-pc-linux-gnu-4.3.6. - - 31 Oct 2012; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> - consed-20-r1.ebuild: - renamed dependency from openmotif to motif consed-20-r1.ebuild, - added some extra patches files/nLine.h.patch, - files/nextPhredPipeline.cpp.patch diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild deleted file mode 100644 index 30ba866..0000000 --- a/sci-biology/consed/consed-20-r1.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die - epatch "${FILESDIR}"/nextPhredPipeline.cpp.patch || die - epatch "${FILESDIR}"/nLine.h.patch || die -} - -src_compile() { - emake || die "If you have gcc-4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild deleted file mode 100644 index b7993b7..0000000 --- a/sci-biology/consed/consed-21.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - doenvd "${S}/99consed" || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-22.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-23.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-24.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-25.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-26.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild deleted file mode 100644 index 4c8dd7f..0000000 --- a/sci-biology/consed/consed-27.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die -} - -src_compile() { - emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler \ - 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 - sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/files/nLine.h.patch b/sci-biology/consed/files/nLine.h.patch deleted file mode 100644 index 9b6779e..0000000 --- a/sci-biology/consed/files/nLine.h.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- nLine.h.ori 2011-04-28 02:12:58.000000000 +0200 -+++ nLine.h 2011-04-28 02:13:43.000000000 +0200 -@@ -44,11 +44,11 @@ - - #ifdef DEFINE_nLine - --int nLine; -+long nLine; - - #else - --extern int nLine; -+extern long nLine; - - #endif - - diff --git a/sci-biology/consed/files/nextPhredPipeline.cpp.patch b/sci-biology/consed/files/nextPhredPipeline.cpp.patch deleted file mode 100644 index 92d4fc0..0000000 --- a/sci-biology/consed/files/nextPhredPipeline.cpp.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- nextPhredPipeline.cpp.ori 2011-01-08 20:44:45.000000000 +0100 -+++ nextPhredPipeline.cpp 2011-01-08 20:47:29.000000000 +0100 -@@ -476,7 +476,7 @@ - void nextPhredPipeline :: openAndLockControlFile() { - - -- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR ); -+ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600 ); - if ( nFDControlFile_ == -1 ) { - THROW_FILE_ERROR( filControlFile_ ); - } diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml deleted file mode 100644 index 3302123..0000000 --- a/sci-biology/consed/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer> - <email>wea...@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> -</pkgmetadata>
