* [gentoo-commits] proj/sci:master commit in: sci-biology/STAR/
@ 2015-05-05 14:04 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-05 14:04 UTC (permalink / raw
To: gentoo-commits
commit: a6c3140a2b483a8bb7fb63a914084e731d68cb39
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 5 14:00:42 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 5 14:00:42 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6c3140a
sci-biology/STAR: new package
Package-Manager: portage-2.2.18
sci-biology/STAR/ChangeLog | 10 ++++++++++
sci-biology/STAR/STAR-2.4.1c.ebuild | 38 +++++++++++++++++++++++++++++++++++++
sci-biology/STAR/STAR-9999.ebuild | 37 ++++++++++++++++++++++++++++++++++++
sci-biology/STAR/metadata.xml | 9 +++++++++
4 files changed, 94 insertions(+)
diff --git a/sci-biology/STAR/ChangeLog b/sci-biology/STAR/ChangeLog
new file mode 100644
index 0000000..b718477
--- /dev/null
+++ b/sci-biology/STAR/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/STAR
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*STAR-2.4.1c (05 May 2015)
+*STAR-9999 (05 May 2015)
+
+ 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +STAR-2.4.1c.ebuild,
+ +STAR-9999.ebuild, +metadata.xml:
+ sci-biology/STAR: new package
diff --git a/sci-biology/STAR/STAR-2.4.1c.ebuild b/sci-biology/STAR/STAR-2.4.1c.ebuild
new file mode 100644
index 0000000..bed7e73
--- /dev/null
+++ b/sci-biology/STAR/STAR-2.4.1c.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
+HOMEPAGE="http://code.google.com/p/rna-star/"
+SRC_URI="https://github.com/alexdobin/STAR/archive/STAR_"${PV}".tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# sci-biology/htslib
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/STAR-STAR_"${PV}"
+
+# contains bundled STAR-Fusion
+src_prepare(){
+ sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
+ sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
+}
+
+src_compile(){
+ cd source || die
+ emake STAR
+}
+
+src_install(){
+ dobin source/STAR
+ dodoc doc/STARmanual.pdf
+}
diff --git a/sci-biology/STAR/STAR-9999.ebuild b/sci-biology/STAR/STAR-9999.ebuild
new file mode 100644
index 0000000..149226a
--- /dev/null
+++ b/sci-biology/STAR/STAR-9999.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit git-r3 toolchain-funcs
+
+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
+HOMEPAGE="http://code.google.com/p/rna-star/"
+EGIT_REPO_URI="https://github.com/alexdobin/STAR.git"
+# http://rna-star.googlecode.com/files/STARmanual_2.3.0.1.pdf
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled version sci-biology/htslib-0.0.1
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+# contains bundled STAR-Fusion
+src_prepare(){
+ sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
+ sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
+}
+
+src_compile(){
+ cd source || die
+ emake STAR
+}
+
+src_install(){
+ dobin source/STAR
+ dodoc doc/STARmanual.pdf
+}
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/STAR/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/STAR/
@ 2017-11-16 17:56 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-11-16 17:56 UTC (permalink / raw
To: gentoo-commits
commit: a27c26fa6cd2fe0cb277ecadc0ece01e8d4fa277
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 16 17:54:47 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 16 17:55:54 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a27c26fa
sci-biology/STAR: In main tree
Package-Manager: Portage-2.3.14, Repoman-2.3.6
sci-biology/STAR/STAR-2.4.1c.ebuild | 37 -------------------------------------
1 file changed, 37 deletions(-)
diff --git a/sci-biology/STAR/STAR-2.4.1c.ebuild b/sci-biology/STAR/STAR-2.4.1c.ebuild
deleted file mode 100644
index c39ea1e22..000000000
--- a/sci-biology/STAR/STAR-2.4.1c.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="http://code.google.com/p/rna-star/"
-SRC_URI="https://github.com/alexdobin/STAR/archive/STAR_"${PV}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# sci-biology/htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/STAR-STAR_"${PV}"
-
-# contains bundled STAR-Fusion
-src_prepare(){
- sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
- sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
-}
-
-src_compile(){
- cd source || die
- emake STAR
-}
-
-src_install(){
- dobin source/STAR
- dodoc doc/STARmanual.pdf
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/STAR/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 3+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
commit: a34f3a93dc9085b7ecb7a7bd7db671351243373c
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 10:43:17 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 10:43:17 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a34f3a93
sci-biology/STAR: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
sci-biology/STAR/STAR-9999.ebuild | 36 ------------------------------------
sci-biology/STAR/metadata.xml | 15 ---------------
2 files changed, 51 deletions(-)
diff --git a/sci-biology/STAR/STAR-9999.ebuild b/sci-biology/STAR/STAR-9999.ebuild
deleted file mode 100644
index 787583b66..000000000
--- a/sci-biology/STAR/STAR-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="http://code.google.com/p/rna-star/"
-EGIT_REPO_URI="https://github.com/alexdobin/STAR.git"
-# http://rna-star.googlecode.com/files/STARmanual_2.3.0.1.pdf
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# contains bundled version sci-biology/htslib-0.0.1
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# contains bundled STAR-Fusion
-src_prepare(){
- sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
- sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
-}
-
-src_compile(){
- cd source || die
- emake STAR
-}
-
-src_install(){
- dobin source/STAR
- dodoc doc/STARmanual.pdf
-}
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
deleted file mode 100644
index 1f2f45f25..000000000
--- a/sci-biology/STAR/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">alexdobin/STAR</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
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