[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: 688791dd334fa90d4d2a87015288141488db54b5 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:26:56 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:26:56 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=688791dd sci-biology/kraken: treeclean Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/kraken/kraken-1.1.1-r2.ebuild | 51 sci-biology/kraken/kraken-2.1.1.ebuild| 55 --- sci-biology/kraken/metadata.xml | 12 --- 3 files changed, 118 deletions(-) diff --git a/sci-biology/kraken/kraken-1.1.1-r2.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild deleted file mode 100644 index 3dd599b83..0 --- a/sci-biology/kraken/kraken-1.1.1-r2.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken"; -SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="1" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - dev-lang/perl - net-misc/wget - sci-biology/jellyfish:1 -" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken.sh || die -} - -src_compile(){ - ./install_kraken.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona"; -} diff --git a/sci-biology/kraken/kraken-2.1.1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild deleted file mode 100644 index 0991f94fa..0 --- a/sci-biology/kraken/kraken-2.1.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken2/"; -SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="2" -KEYWORDS="~amd64" - -# TODO: somehow avoid the file conflict with kraken-1 -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/ncbi-tools++ - dev-lang/perl - net-misc/wget - !sci-biology/kraken:1 -" - -S="${WORKDIR}/${PN}2-${PV}" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken2.sh || die -} - -src_compile(){ - ./install_kraken2.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona"; -} diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml deleted file mode 100644 index 138cb7705..0 --- a/sci-biology/kraken/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - -http://www.gentoo.org/dtd/metadata.dtd";> - - - mmokr...@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biol...@gentoo.org - Gentoo Biology Project - -
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: 864b2c5e4f51a2894e0a87dbf777c2c056a2cfa1 Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Mar 23 09:27:19 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Tue Mar 23 09:27:19 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=864b2c5e sci-biology/kraken: add kraken version 2 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> ...raken-1.1.1-r1.ebuild => kraken-1.1.1-r2.ebuild} | 9 +++-- .../{kraken-1.1.1-r1.ebuild => kraken-2.1.1.ebuild} | 21 +++-- 2 files changed, 14 insertions(+), 16 deletions(-) diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild similarity index 85% copy from sci-biology/kraken/kraken-1.1.1-r1.ebuild copy to sci-biology/kraken/kraken-1.1.1-r2.ebuild index fb97ab47e..3dd599b83 100644 --- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1-r2.ebuild @@ -7,11 +7,10 @@ inherit perl-functions DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" HOMEPAGE="https://ccb.jhu.edu/software/kraken"; -SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz - https://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" +SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" -SLOT="0" +SLOT="1" KEYWORDS="~amd64" DEPEND="" @@ -21,8 +20,6 @@ RDEPEND="${DEPEND} sci-biology/jellyfish:1 " -S="${WORKDIR}/${PN}-1.0" - src_prepare(){ default sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die @@ -34,7 +31,7 @@ src_compile(){ } src_install(){ - dodoc "${DISTDIR}/${P}_MANUAL.html" + dodoc -r docs perl_set_version perl_domodule destdir/*.pm dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild similarity index 74% rename from sci-biology/kraken/kraken-1.1.1-r1.ebuild rename to sci-biology/kraken/kraken-2.1.1.ebuild index fb97ab47e..0991f94fa 100644 --- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild +++ b/sci-biology/kraken/kraken-2.1.1.ebuild @@ -6,35 +6,36 @@ EAPI=7 inherit perl-functions DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken"; -SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz - https://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" +HOMEPAGE="https://ccb.jhu.edu/software/kraken2/"; +SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" -LICENSE="GPL-3" -SLOT="0" +LICENSE="MIT" +SLOT="2" KEYWORDS="~amd64" +# TODO: somehow avoid the file conflict with kraken-1 DEPEND="" RDEPEND="${DEPEND} + sci-biology/ncbi-tools++ dev-lang/perl net-misc/wget - sci-biology/jellyfish:1 + !sci-biology/kraken:1 " -S="${WORKDIR}/${PN}-1.0" +S="${WORKDIR}/${PN}2-${PV}" src_prepare(){ default sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken.sh || die + echo "exit 0" >> install_kraken2.sh || die } src_compile(){ - ./install_kraken.sh destdir || die + ./install_kraken2.sh destdir || die } src_install(){ - dodoc "${DISTDIR}/${P}_MANUAL.html" + dodoc -r docs perl_set_version perl_domodule destdir/*.pm dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: c4b5bd1286da6184d34b15463223b0aa6ca3a1d4 Author: Andrew Ammerlaan riseup net> AuthorDate: Thu Mar 18 20:26:54 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Thu Mar 18 20:26:54 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c4b5bd12 sci-biology/kraken: fix symlink in prefix Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/kraken/kraken-1.1.1-r1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-1.1.1-r1.ebuild index 788670b63..fb97ab47e 100644 --- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1-r1.ebuild @@ -37,7 +37,7 @@ src_install(){ dodoc "${DISTDIR}/${P}_MANUAL.html" perl_set_version perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB}/krakenlib.pm" /usr/bin/krakenlib.pm + dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm insinto /usr/share/${PN}/util doins destdir/*.pl chmod -R a+rx "${ED}/usr/share/${PN}/util"
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: 4e6eeb8668601981b658634da13daa25a9359a67 Author: Andrew Ammerlaan riseup net> AuthorDate: Thu Mar 18 19:47:30 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Thu Mar 18 19:47:30 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e6eeb86 sci-biology/kraken: add symlink Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/kraken/{kraken-1.1.1.ebuild => kraken-1.1.1-r1.ebuild} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sci-biology/kraken/kraken-1.1.1.ebuild b/sci-biology/kraken/kraken-1.1.1-r1.ebuild similarity index 94% rename from sci-biology/kraken/kraken-1.1.1.ebuild rename to sci-biology/kraken/kraken-1.1.1-r1.ebuild index d132b6db7..788670b63 100644 --- a/sci-biology/kraken/kraken-1.1.1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1-r1.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit perl-module +inherit perl-functions DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" HOMEPAGE="https://ccb.jhu.edu/software/kraken"; @@ -37,6 +37,7 @@ src_install(){ dodoc "${DISTDIR}/${P}_MANUAL.html" perl_set_version perl_domodule destdir/*.pm + dosym ../../"${VENDOR_LIB}/krakenlib.pm" /usr/bin/krakenlib.pm insinto /usr/share/${PN}/util doins destdir/*.pl chmod -R a+rx "${ED}/usr/share/${PN}/util"
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: d9efa2d88a0709b8141ee155d5d2e2e1ed3b0005 Author: Andrew Ammerlaan riseup net> AuthorDate: Thu Mar 18 18:52:04 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Thu Mar 18 18:52:04 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9efa2d8 sci-biology/kraken: use perl_domodule Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/kraken/kraken-1.1.1.ebuild | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/sci-biology/kraken/kraken-1.1.1.ebuild b/sci-biology/kraken/kraken-1.1.1.ebuild index c5e8584b2..d132b6db7 100644 --- a/sci-biology/kraken/kraken-1.1.1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1.ebuild @@ -36,8 +36,7 @@ src_compile(){ src_install(){ dodoc "${DISTDIR}/${P}_MANUAL.html" perl_set_version - insinto ${VENDOR_LIB}/${PN} - doins destdir/*.pm + perl_domodule destdir/*.pm insinto /usr/share/${PN}/util doins destdir/*.pl chmod -R a+rx "${ED}/usr/share/${PN}/util"
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: a0fa80290ded3e7cd5085b60d49e115e7b2469d9 Author: Andrew Ammerlaan riseup net> AuthorDate: Wed Mar 17 21:29:25 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Wed Mar 17 21:29:57 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0fa8029 sci-biology/kraken: use ED variable Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/kraken/kraken-1.1.1.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/kraken/kraken-1.1.1.ebuild b/sci-biology/kraken/kraken-1.1.1.ebuild index 47ca1b86e..c5e8584b2 100644 --- a/sci-biology/kraken/kraken-1.1.1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1.ebuild @@ -34,13 +34,13 @@ src_compile(){ } src_install(){ - dodoc "${DISTDIR}"/${P}_MANUAL.html + dodoc "${DISTDIR}/${P}_MANUAL.html" perl_set_version insinto ${VENDOR_LIB}/${PN} doins destdir/*.pm insinto /usr/share/${PN}/util doins destdir/*.pl - chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util + chmod -R a+rx "${ED}/usr/share/${PN}/util" rm -f destdir/krakenlib.pm dobin destdir/* }
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: 0e960307417d5306f51c0d73c00c4a68cd47e529 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Nov 24 21:36:55 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Nov 24 21:36:55 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e960307 sci-biology/kraken: version bump Package-Manager: Portage-2.3.14, Repoman-2.3.6 sci-biology/kraken/{kraken-0.10.5.ebuild => kraken-1.0.ebuild} | 10 -- 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/sci-biology/kraken/kraken-0.10.5.ebuild b/sci-biology/kraken/kraken-1.0.ebuild similarity index 85% rename from sci-biology/kraken/kraken-0.10.5.ebuild rename to sci-biology/kraken/kraken-1.0.ebuild index d5fb4545e..b579a7eef 100644 --- a/sci-biology/kraken/kraken-0.10.5.ebuild +++ b/sci-biology/kraken/kraken-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -9,8 +9,8 @@ inherit perl-module DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" HOMEPAGE="http://ccb.jhu.edu/software/kraken http://genomebiology.com/2014/15/3/R46"; -SRC_URI="http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz - http://ccb.jhu.edu/software/kraken/MANUAL.html"; +SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz + http://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" LICENSE="GPL-3" SLOT="0" @@ -22,8 +22,6 @@ RDEPEND="${DEPEND} dev-lang/perl net-misc/wget" -S="${WORKDIR}"/kraken-0.10.5-beta - src_prepare(){ sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die echo "exit 0" >> install_kraken.sh || die @@ -34,7 +32,7 @@ src_compile(){ } src_install(){ - dohtml "${DISTDIR}"/MANUAL.html + dohtml "${DISTDIR}"/${P}_MANUAL.html perl_set_version insinto ${VENDOR_LIB}/${PN} doins destdir/*.pm
[gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
commit: 94465f706e18530fe400311e03ae114e59a679af Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 30 21:19:52 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 30 21:19:52 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=94465f70 sci-biology/kraken: new package with huge requirements Package-Manager: portage-2.2.28 sci-biology/kraken/kraken-0.10.5.ebuild | 55 + sci-biology/kraken/metadata.xml | 12 +++ 2 files changed, 67 insertions(+) diff --git a/sci-biology/kraken/kraken-0.10.5.ebuild b/sci-biology/kraken/kraken-0.10.5.ebuild new file mode 100644 index 000..540c73d --- /dev/null +++ b/sci-biology/kraken/kraken-0.10.5.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module + +DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" +HOMEPAGE="http://ccb.jhu.edu/software/kraken + http://genomebiology.com/2014/15/3/R46"; +SRC_URI="http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz + http://ccb.jhu.edu/software/kraken/MANUAL.html"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + net-misc/wget" + +S="${WORKDIR}"/kraken-0.10.5-beta + +src_prepare(){ + sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die + echo "exit 0" >> install_kraken.sh || die +} + +src_compile(){ + ./install_kraken.sh destdir || die +} + +src_install(){ + dohtml "${DISTDIR}"/MANUAL.html + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins destdir/*.pm + insinto /usr/share/${PN}/util + doins destdir/*.pl + chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util + rm -f destdir/krakenlib.pm + dobin destdir/* +} + +pkg_postinst(){ + ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" + ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" + ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" + ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" + ewarn "Results can be visualized with http://sourceforge.net/p/krona/home/krona"; +} diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml new file mode 100644 index 000..f68a1b6 --- /dev/null +++ b/sci-biology/kraken/metadata.xml @@ -0,0 +1,12 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + +mmokr...@fold.natur.cuni.cz +Martin Mokrejs + + +sci-biol...@gentoo.org +Gentoo Biology Project + +