* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-02-10 13:31 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-02-10 13:31 UTC (permalink / raw
To: gentoo-commits
commit: 1a4dc5be8fd24487de1306cf68af5a7d507edb01
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 13:28:39 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 13:28:39 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a4dc5be
sci-biology/SnpEff: version bump
Package-Manager: portage-2.2.26
sci-biology/SnpEff/SnpEff-4.1e.ebuild | 56 +++++++++++++++++++++++++++++++++++
sci-biology/SnpEff/metadata.xml | 9 ++++++
2 files changed, 65 insertions(+)
diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
new file mode 100644
index 0000000..5e9434a
--- /dev/null
+++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Annotate SNP changes and predict their effect"
+HOMEPAGE="http://snpeff.sourceforge.net"
+
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git"
+ #EGIT_BRANCH="v4.1B"
+ KEYWORDS=""
+else
+ SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
+ http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
+ KEYWORDS="~amd64"
+ S="${WORKDIR}"
+fi
+
+LICENSE="LGPL-3"
+SLOT="0"
+IUSE=""
+
+# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
+DEPEND=">=virtual/jre-1.7:*
+ dev-java/maven-bin:*
+ dev-java/antlr:*"
+RDEPEND="${DEPEND}
+ >=virtual/jdk-1.7:*"
+
+#src_compile(){
+# mvn || die
+#}
+
+src_install(){
+ cd .. || die
+ mkdir -p "${D}"/usr/share
+ # but portage does not install the .* files and subdirs, grr!
+ unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
+ sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+}
+
+# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/
+# it also automagically fetches them but into /tmp/ unlike $CWD
+#
+# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf
+#
+# It is best to just unpack the tarball locally and not use portage at all.
diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/SnpEff/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-02-14 17:32 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2016-02-14 17:32 UTC (permalink / raw
To: gentoo-commits
commit: b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 14 17:17:02 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 14 17:17:16 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b39edea7
sci-biology/SnpEff: Bump to EAPI=6
* Clean multiverion code
Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/SnpEff/SnpEff-4.1e.ebuild | 48 +++++++++++++++++++----------------
sci-biology/SnpEff/metadata.xml | 2 +-
2 files changed, 27 insertions(+), 23 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
index 5e9434a..7ba4236 100644
--- a/sci-biology/SnpEff/SnpEff-4.1e.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
@@ -1,51 +1,55 @@
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2 java-ant-2
-[ "$PV" == "9999" ] && inherit git-2
-
DESCRIPTION="Annotate SNP changes and predict their effect"
HOMEPAGE="http://snpeff.sourceforge.net"
-
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git"
- #EGIT_BRANCH="v4.1B"
- KEYWORDS=""
-else
- SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
- http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
- KEYWORDS="~amd64"
- S="${WORKDIR}"
-fi
+SRC_URI="
+ http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
+ http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
LICENSE="LGPL-3"
SLOT="0"
+KEYWORDS="~amd64"
IUSE=""
# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
-DEPEND=">=virtual/jre-1.7:*
+DEPEND="
+ >=virtual/jre-1.7:*
dev-java/maven-bin:*
dev-java/antlr:*"
RDEPEND="${DEPEND}
>=virtual/jdk-1.7:*"
+ S="${WORKDIR}"
+
#src_compile(){
# mvn || die
#}
src_install(){
cd .. || die
- mkdir -p "${D}"/usr/share
+ mkdir -p "${D}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
- unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
- sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
- sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
- sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
- sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ unzip \
+ "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share \
+ || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
+ sed \
+ -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
+ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed \
+ -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' \
+ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed \
+ -e 's#$HOME/snpEff/#/usr/share/snpEff/#' \
+ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+ sed \
+ -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' \
+ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
}
# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/
diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/SnpEff/metadata.xml
+++ b/sci-biology/SnpEff/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-07-27 8:56 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-07-27 8:56 UTC (permalink / raw
To: gentoo-commits
commit: 84e0f638f095e67e26939f1f33c16c115745edca
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul 27 08:56:40 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul 27 08:56:40 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=84e0f638
sci-biology/SnpEff: version bump
Package-Manager: portage-2.2.28
sci-biology/SnpEff/{SnpEff-4.1e.ebuild => SnpEff-4.2.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.2.ebuild
similarity index 92%
rename from sci-biology/SnpEff/SnpEff-4.1e.ebuild
rename to sci-biology/SnpEff/SnpEff-4.2.ebuild
index 7ba4236..ecdc205 100644
--- a/sci-biology/SnpEff/SnpEff-4.1e.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.2.ebuild
@@ -9,7 +9,7 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Annotate SNP changes and predict their effect"
HOMEPAGE="http://snpeff.sourceforge.net"
SRC_URI="
- http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
+ http://sourceforge.net/projects/snpeff/files/snpEff_v4_2_core.zip
http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
LICENSE="LGPL-3"
@@ -37,7 +37,7 @@ src_install(){
# but portage does not install the .* files and subdirs, grr!
unzip \
"${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share \
- || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
+ || die "failed to unzip ${DISTDIR}/snpEff_v4_2_core.zip"
sed \
-e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-07-31 22:15 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-07-31 22:15 UTC (permalink / raw
To: gentoo-commits
commit: 556f260e90750a3919e5fb0167d0ce7285f3d7ac
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 22:14:49 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 22:14:49 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=556f260e
sci-biology/SnpEff: fix indentation
Package-Manager: portage-2.3.0
sci-biology/SnpEff/SnpEff-4.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.2.ebuild b/sci-biology/SnpEff/SnpEff-4.2.ebuild
index ecdc205..9272b63 100644
--- a/sci-biology/SnpEff/SnpEff-4.2.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.2.ebuild
@@ -25,7 +25,7 @@ DEPEND="
RDEPEND="${DEPEND}
>=virtual/jdk-1.7:*"
- S="${WORKDIR}"
+S="${WORKDIR}"
#src_compile(){
# mvn || die
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-08-01 12:44 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-08-01 12:44 UTC (permalink / raw
To: gentoo-commits
commit: 29d62487d6b5776402688fee78b2dbb47cdf3e5c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug 1 12:43:59 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug 1 12:43:59 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=29d62487
sci-biology/SnpEff: re-order dependencies, back to EAPI=5
Package-Manager: portage-2.3.0
sci-biology/SnpEff/SnpEff-4.2.ebuild | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.2.ebuild b/sci-biology/SnpEff/SnpEff-4.2.ebuild
index 9272b63..7cdd51c 100644
--- a/sci-biology/SnpEff/SnpEff-4.2.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.2.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=6
+EAPI=5
inherit java-pkg-2 java-ant-2
@@ -18,12 +18,13 @@ KEYWORDS="~amd64"
IUSE=""
# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
-DEPEND="
+RDEPEND="
>=virtual/jre-1.7:*
dev-java/maven-bin:*
dev-java/antlr:*"
-RDEPEND="${DEPEND}
- >=virtual/jdk-1.7:*"
+DEPEND="${RDEPEND}
+ >=virtual/jdk-1.7:*
+ dev-java/ant-core"
S="${WORKDIR}"
@@ -36,7 +37,7 @@ src_install(){
mkdir -p "${D}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
unzip \
- "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share \
+ "${DISTDIR}"/snpEff_v4_2_core.zip -d "${D}"/usr/share \
|| die "failed to unzip ${DISTDIR}/snpEff_v4_2_core.zip"
sed \
-e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-12-07 10:00 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-12-07 10:00 UTC (permalink / raw
To: gentoo-commits
commit: e5cf10b0eb4504480f9e6a26e4b11de229e3e37a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 10:00:10 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 10:00:10 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5cf10b0
sci-biology/SnpEff: version bump, may be moved to our main repo
Package-Manager: portage-2.3.2
.../SnpEff/{SnpEff-4.2.ebuild => SnpEff-4.3g.ebuild} | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.2.ebuild b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
similarity index 81%
rename from sci-biology/SnpEff/SnpEff-4.2.ebuild
rename to sci-biology/SnpEff/SnpEff-4.3g.ebuild
index 7cdd51c..f817588 100644
--- a/sci-biology/SnpEff/SnpEff-4.2.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
@@ -2,19 +2,21 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Annotate SNP changes and predict their effect"
+MY_PV=${PV/./_}
+
+DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
HOMEPAGE="http://snpeff.sourceforge.net"
SRC_URI="
- http://sourceforge.net/projects/snpeff/files/snpEff_v4_2_core.zip
+ http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
LICENSE="LGPL-3"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
@@ -37,8 +39,8 @@ src_install(){
mkdir -p "${D}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
unzip \
- "${DISTDIR}"/snpEff_v4_2_core.zip -d "${D}"/usr/share \
- || die "failed to unzip ${DISTDIR}/snpEff_v4_2_core.zip"
+ "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${D}"/usr/share \
+ || die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
sed \
-e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2016-12-07 10:15 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-12-07 10:15 UTC (permalink / raw
To: gentoo-commits
commit: 5fb831e8c3bcf4b192b96dcf018a558a86bd1581
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 10:14:58 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 10:14:58 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5fb831e8
sci-biology/SnpEff: fix installation on PREFIX
Package-Manager: portage-2.3.2
sci-biology/SnpEff/SnpEff-4.3g.ebuild | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.3g.ebuild b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
index f817588..fb11894 100644
--- a/sci-biology/SnpEff/SnpEff-4.3g.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
@@ -36,22 +36,22 @@ S="${WORKDIR}"
src_install(){
cd .. || die
- mkdir -p "${D}"/usr/share || die
+ mkdir -p "${ED}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
unzip \
- "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${D}"/usr/share \
+ "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \
|| die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
sed \
- -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
+ -e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
- -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' \
+ -e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
- -e 's#$HOME/snpEff/#/usr/share/snpEff/#' \
+ -e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
- -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' \
+ -e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2017-02-20 22:50 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-02-20 22:50 UTC (permalink / raw
To: gentoo-commits
commit: 48b67e4f7b81d20f6f0454c1e329454991c0aa5b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 22:50:36 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 22:50:36 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=48b67e4f
sci-biology/SnpEff: version bump
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/SnpEff/{SnpEff-4.3g.ebuild => SnpEff-4.3i.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.3g.ebuild b/sci-biology/SnpEff/SnpEff-4.3i.ebuild
similarity index 97%
rename from sci-biology/SnpEff/SnpEff-4.3g.ebuild
rename to sci-biology/SnpEff/SnpEff-4.3i.ebuild
index fb1189406..8d2a06821 100644
--- a/sci-biology/SnpEff/SnpEff-4.3g.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3i.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
# $Id$
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/
@ 2021-01-24 13:54 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 13:54 UTC (permalink / raw
To: gentoo-commits
commit: 843b1f675001ddf24cf56c5b0e9dcd3680111cef
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 13:51:53 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 13:54:11 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=843b1f67
sci-biology/SnpEff: fix install
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/SnpEff/SnpEff-4.3t.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
index ddece0256..843c00356 100644
--- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
@@ -13,7 +13,7 @@ SRC_URI="
LICENSE="LGPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
RDEPEND="
>=virtual/jre-1.7:*
@@ -31,8 +31,8 @@ src_install(){
mkdir -p "${ED}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
unzip \
- "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \
- || die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
+ "${DISTDIR}"/snpEff_v"${PV//./_}"_core.zip -d "${ED}"/usr/share \
+ || die "failed to unzip ${DISTDIR}/snpEff_v${PV//./_}_core.zip"
sed \
-e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
^ permalink raw reply related [flat|nested] 9+ messages in thread
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2016-12-07 10:15 Martin Mokrejs
2016-12-07 10:00 Martin Mokrejs
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2016-07-31 22:15 Martin Mokrejs
2016-07-27 8:56 Martin Mokrejs
2016-02-14 17:32 Justin Lecher
2016-02-10 13:31 Martin Mokrejs
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