* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2021-03-17 21:29 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-17 21:29 UTC (permalink / raw
To: gentoo-commits
commit: a0fa80290ded3e7cd5085b60d49e115e7b2469d9
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Mar 17 21:29:25 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Mar 17 21:29:57 2021 +0000
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 <andrewammerlaan <AT> 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/*
}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2023-05-02 12:27 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:27 UTC (permalink / raw
To: gentoo-commits
commit: 688791dd334fa90d4d2a87015288141488db54b5
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:26:56 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:26:56 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=688791dd
sci-biology/kraken: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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..000000000
--- 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/${PN}/util"
- rm -f destdir/krakenlib.pm
- dobin destdir/*
-}
-
-pkg_postinst(){
- ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs"
- ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read"
- ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space"
- ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM"
- ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona"
-}
diff --git a/sci-biology/kraken/kraken-2.1.1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild
deleted file mode 100644
index 0991f94fa..000000000
--- a/sci-biology/kraken/kraken-2.1.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
-HOMEPAGE="https://ccb.jhu.edu/software/kraken2/"
-SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${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..000000000
--- a/sci-biology/kraken/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2021-03-23 9:27 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-23 9:27 UTC (permalink / raw
To: gentoo-commits
commit: 864b2c5e4f51a2894e0a87dbf777c2c056a2cfa1
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 23 09:27:19 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 23 09:27:19 2021 +0000
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 <andrewammerlaan <AT> 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//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2021-03-18 20:27 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 20:27 UTC (permalink / raw
To: gentoo-commits
commit: c4b5bd1286da6184d34b15463223b0aa6ca3a1d4
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 20:26:54 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 20:26:54 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c4b5bd12
sci-biology/kraken: fix symlink in prefix
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kraken/kraken-1.1.1-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-1.1.1-r1.ebuild
index 788670b63..fb97ab47e 100644
--- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild
+++ b/sci-biology/kraken/kraken-1.1.1-r1.ebuild
@@ -37,7 +37,7 @@ src_install(){
dodoc "${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/${PN}/util"
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2021-03-18 19:47 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 19:47 UTC (permalink / raw
To: gentoo-commits
commit: 4e6eeb8668601981b658634da13daa25a9359a67
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 19:47:30 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 19:47:30 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e6eeb86
sci-biology/kraken: add symlink
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kraken/{kraken-1.1.1.ebuild => kraken-1.1.1-r1.ebuild} | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/kraken/kraken-1.1.1.ebuild b/sci-biology/kraken/kraken-1.1.1-r1.ebuild
similarity index 94%
rename from sci-biology/kraken/kraken-1.1.1.ebuild
rename to sci-biology/kraken/kraken-1.1.1-r1.ebuild
index d132b6db7..788670b63 100644
--- a/sci-biology/kraken/kraken-1.1.1.ebuild
+++ b/sci-biology/kraken/kraken-1.1.1-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit perl-module
+inherit perl-functions
DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
HOMEPAGE="https://ccb.jhu.edu/software/kraken"
@@ -37,6 +37,7 @@ src_install(){
dodoc "${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/${PN}/util"
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: d9efa2d88a0709b8141ee155d5d2e2e1ed3b0005
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:52:04 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:52:04 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9efa2d8
sci-biology/kraken: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kraken/kraken-1.1.1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/kraken/kraken-1.1.1.ebuild b/sci-biology/kraken/kraken-1.1.1.ebuild
index c5e8584b2..d132b6db7 100644
--- a/sci-biology/kraken/kraken-1.1.1.ebuild
+++ b/sci-biology/kraken/kraken-1.1.1.ebuild
@@ -36,8 +36,7 @@ src_compile(){
src_install(){
dodoc "${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"
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2017-11-24 21:37 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2017-11-24 21:37 UTC (permalink / raw
To: gentoo-commits
commit: 0e960307417d5306f51c0d73c00c4a68cd47e529
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 24 21:36:55 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 24 21:36:55 2017 +0000
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
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
@ 2016-06-30 21:20 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-06-30 21:20 UTC (permalink / raw
To: gentoo-commits
commit: 94465f706e18530fe400311e03ae114e59a679af
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 21:19:52 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 21:19:52 2016 +0000
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 0000000..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 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/kraken/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread
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