* [gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
@ 2016-04-10 20:23 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-04-10 20:23 UTC (permalink / raw
To: gentoo-commits
commit: a81192976249025c253af5645ce2510992f899a9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 20:20:53 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 20:20:53 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a8119297
sci-biology/somatic-sniper: new package
Package-Manager: portage-2.2.28
sci-biology/somatic-sniper/metadata.xml | 12 +++++++++
.../somatic-sniper/somatic-sniper-1.0.4.ebuild | 29 ++++++++++++++++++++++
2 files changed, 41 insertions(+)
diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/somatic-sniper/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>
diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
new file mode 100644
index 0000000..e4629b6
--- /dev/null
+++ b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs"
+HOMEPAGE="http://gmt.genome.wustl.edu"
+SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+# git clone git://github.com/genome/somatic-sniper.git
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ sys-libs/zlib
+ sys-libs/ncurses:*
+ sci-biology/samtools:0.1-legacy"
+RDEPEND="${DEPEND}"
+
+# contains bundled copy of samtools-0.1.6 but links using a static version
+# cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1
+# /usr/bin/x86_64-pc-linux-gnu-gcc -Wall -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz
+
+# contains build-common from git tree
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
@ 2018-01-20 21:26 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2018-01-20 21:26 UTC (permalink / raw
To: gentoo-commits
commit: d4a7e82783674cb4ba680db8a27c056723632c67
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:25:10 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:25:10 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4a7e827
sci-biology/somatic-sniper: switch git:// to https://
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
index 4432793c2..51a4b9db8 100644
--- a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
+++ b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,7 +8,7 @@ inherit cmake-utils
DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs"
HOMEPAGE="http://gmt.genome.wustl.edu"
SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-# git clone git://github.com/genome/somatic-sniper.git
+# git clone https://github.com/genome/somatic-sniper.git
LICENSE="MIT"
SLOT="0"
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
@ 2021-01-26 21:20 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2021-01-26 21:20 UTC (permalink / raw
To: gentoo-commits
commit: 4a01263f019d66b8e42c4caa45f33a4fae99fb2e
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 26 21:19:37 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 26 21:19:37 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a01263f
sci-biology/somatic-sniper: remove pack, archived upstream
does not build, needs static libs of samtools
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/somatic-sniper/metadata.xml | 15 ------------
.../somatic-sniper/somatic-sniper-1.0.4.ebuild | 28 ----------------------
2 files changed, 43 deletions(-)
diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml
deleted file mode 100644
index ff905cc3e..000000000
--- a/sci-biology/somatic-sniper/metadata.xml
+++ /dev/null
@@ -1,15 +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>
- <upstream>
- <remote-id type="github">genome/somatic-sniper</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
deleted file mode 100644
index 51a4b9db8..000000000
--- a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs"
-HOMEPAGE="http://gmt.genome.wustl.edu"
-SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-# git clone https://github.com/genome/somatic-sniper.git
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
- sys-libs/zlib
- sys-libs/ncurses:*
- sci-biology/samtools:0.1-legacy"
-RDEPEND="${DEPEND}"
-
-# contains bundled copy of samtools-0.1.6 but links using a static version
-# cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1
-# /usr/bin/x86_64-pc-linux-gnu-gcc -Wall -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz
-
-# contains build-common from git tree
^ permalink raw reply related [flat|nested] 3+ messages in thread
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