* [gentoo-commits] proj/sci:master commit in: sci-biology/germline/
@ 2016-08-26 8:45 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-08-26 8:45 UTC (permalink / raw
To: gentoo-commits
commit: 12cca09b9ad1ee543efaf15e08be3deb844fd741
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 26 08:45:50 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 26 08:45:50 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=12cca09b
sci-biology/germline: new package
Package-Manager: portage-2.3.0
sci-biology/germline/germline-1.5.1.ebuild | 35 ++++++++++++++++++++++++++++++
sci-biology/germline/metadata.xml | 12 ++++++++++
2 files changed, 47 insertions(+)
diff --git a/sci-biology/germline/germline-1.5.1.ebuild b/sci-biology/germline/germline-1.5.1.ebuild
new file mode 100644
index 0000000..e2402fc
--- /dev/null
+++ b/sci-biology/germline/germline-1.5.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit versionator toolchain-funcs
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
+HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
+ http://genome.cshlp.org/content/19/2/318.full"
+SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}-${MY_PV}
+
+src_prepare(){
+ sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
+ sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
+ sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
+ default
+}
+
+src_install(){
+ dobin germline parse_bmatch
+}
diff --git a/sci-biology/germline/metadata.xml b/sci-biology/germline/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/germline/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>
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/germline/
@ 2016-09-23 17:35 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-09-23 17:35 UTC (permalink / raw
To: gentoo-commits
commit: ff1f85519180af8eef93cd641ff1fd06fbf7909a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 23 17:35:42 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 23 17:35:42 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff1f8551
sci-biology/germline: version bump
Package-Manager: portage-2.3.0
sci-biology/germline/germline-1.5.2.ebuild | 36 ++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/sci-biology/germline/germline-1.5.2.ebuild b/sci-biology/germline/germline-1.5.2.ebuild
new file mode 100644
index 0000000..b3b681b
--- /dev/null
+++ b/sci-biology/germline/germline-1.5.2.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit versionator toolchain-funcs
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
+HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
+ http://genome.cshlp.org/content/19/2/318.full"
+SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}-${MY_PV}
+
+src_prepare(){
+ sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
+ sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
+ sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
+ default
+}
+
+src_install(){
+ dobin germline parse_bmatch
+ dodoc README
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/germline/
@ 2021-01-24 14:34 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 14:34 UTC (permalink / raw
To: gentoo-commits
commit: 8b619eeb663750fa7dfc2b674eb16505ec788c8d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:34:46 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:34:46 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b619eeb
sci-biology/germline: version bump, EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/germline/germline-1.5.1.ebuild | 34 ----------------------
...germline-1.5.2.ebuild => germline-1.5.3.ebuild} | 15 ++++------
2 files changed, 6 insertions(+), 43 deletions(-)
diff --git a/sci-biology/germline/germline-1.5.1.ebuild b/sci-biology/germline/germline-1.5.1.ebuild
deleted file mode 100644
index 1a9063ee5..000000000
--- a/sci-biology/germline/germline-1.5.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit versionator toolchain-funcs
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
-HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
- http://genome.cshlp.org/content/19/2/318.full"
-SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-libs/boost"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-src_prepare(){
- sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
- sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
- sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
- default
-}
-
-src_install(){
- dobin germline parse_bmatch
-}
diff --git a/sci-biology/germline/germline-1.5.2.ebuild b/sci-biology/germline/germline-1.5.3.ebuild
similarity index 71%
rename from sci-biology/germline/germline-1.5.2.ebuild
rename to sci-biology/germline/germline-1.5.3.ebuild
index c7c5f8396..0363b8fa8 100644
--- a/sci-biology/germline/germline-1.5.2.ebuild
+++ b/sci-biology/germline/germline-1.5.3.ebuild
@@ -1,26 +1,23 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit versionator toolchain-funcs
-
-MY_PV=$(replace_all_version_separators '-')
+inherit toolchain-funcs
DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
-HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
+HOMEPAGE="http://gusevlab.org/projects/germline/
http://genome.cshlp.org/content/19/2/318.full"
-SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
+SRC_URI="http://gusevlab.org/projects/${PN}/release/${PN}-${PV//./-}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND="dev-libs/boost"
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/${PN}-${MY_PV}
+S="${WORKDIR}"/${PN}-${PV//./-}
src_prepare(){
sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
^ permalink raw reply related [flat|nested] 3+ messages in thread
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