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
