[gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
commit: 4a01263f019d66b8e42c4caa45f33a4fae99fb2e
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 26 21:19:37 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 26 21:19:37 2021 +
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 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..0
--- a/sci-biology/somatic-sniper/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- genome/somatic-sniper
-
-
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..0
--- 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
[gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
commit: d4a7e82783674cb4ba680db8a27c056723632c67
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat Jan 20 21:25:10 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Jan 20 21:25:10 2018 +
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"
[gentoo-commits] proj/sci:master commit in: sci-biology/somatic-sniper/
commit: a81192976249025c253af5645ce2510992f899a9
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 10 20:20:53 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 10 20:20:53 2016 +
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 000..f68a1b6
--- /dev/null
+++ b/sci-biology/somatic-sniper/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
+
+
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 000..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
