* [gentoo-commits] proj/sci:master commit in: sci-biology/angsd/
@ 2017-05-01 8:00 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-05-01 8:00 UTC (permalink / raw
To: gentoo-commits
commit: ccf3537c7d36e38e352e4a38c541a292ed139a1d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 1 08:00:28 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 1 08:00:28 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccf3537c
sci-biology/angsd: add default() to make EAPI=6 happy
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/angsd/angsd-9999.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
index 1670e6684..97f614509 100644
--- a/sci-biology/angsd/angsd-9999.ebuild
+++ b/sci-biology/angsd/angsd-9999.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
EAPI=6
@@ -21,6 +21,7 @@ RDEPEND="${DEPEND}"
# https://github.com/ANGSD/angsd/issues/9
src_prepare(){
+ default
sed \
-e 's@FLAGS=-O3@FLAGS=@' \
-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/angsd/
@ 2021-03-05 21:44 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-03-05 21:44 UTC (permalink / raw
To: gentoo-commits
commit: 86735d1722487884f59d66e02e532387cbcbf950
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar 5 21:37:03 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar 5 21:37:03 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=86735d17
sci-biology/angsd: EAPI bump, add 0.933, add keywords
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../angsd/{angsd-9999.ebuild => angsd-0.933.ebuild} | 17 +++++++----------
1 file changed, 7 insertions(+), 10 deletions(-)
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-0.933.ebuild
similarity index 71%
rename from sci-biology/angsd/angsd-9999.ebuild
rename to sci-biology/angsd/angsd-0.933.ebuild
index a4711d244..9a37d2af6 100644
--- a/sci-biology/angsd/angsd-9999.ebuild
+++ b/sci-biology/angsd/angsd-0.933.ebuild
@@ -1,18 +1,15 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-
-inherit git-r3
+EAPI=7
DESCRIPTION="Population genetics analysis package"
HOMEPAGE="http://www.popgen.dk/angsd"
-EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
+SRC_URI="https://github.com/ANGSD/angsd/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
DEPEND="
dev-lang/R
@@ -41,10 +38,10 @@ src_compile(){
}
src_install(){
+ einstalldocs
dobin angsd
- dodoc README.md
cd misc || die
dobin \
- supersim thetaStat realSFS emOptim2 msToGlf smartCount \
- printIcounts splitgl contamination NGSadmix
+ supersim haploToPlink ibs thetaStat realSFS msToGlf msHOT2glf smartCount \
+ printIcounts splitgl contamination contamination2 NGSadmix ngsPSMC scounts
}
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/angsd/
@ 2016-02-14 17:32 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2016-02-14 17:32 UTC (permalink / raw
To: gentoo-commits
commit: 10febb5681bdc497d34f2c58667e31124437fa65
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 14 17:32:26 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 14 17:32:35 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=10febb56
sci-biology/angsd: Bump to EAPI=6
* Use git-r3.eclass
Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/angsd/angsd-9999.ebuild | 41 +++++++++++++++++++------------------
sci-biology/angsd/metadata.xml | 2 +-
2 files changed, 22 insertions(+), 21 deletions(-)
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
index e4c2be6..0de57d4 100644
--- a/sci-biology/angsd/angsd-9999.ebuild
+++ b/sci-biology/angsd/angsd-9999.ebuild
@@ -1,40 +1,39 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
-inherit git-2
-
-[ "$PV" == "9999" ] && inherit git-2
+inherit git-r3
DESCRIPTION="Population genetics analysis package"
HOMEPAGE="http://www.popgen.dk/angsd"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
- KEYWORDS=""
-else
- EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
- EGIT_BRANCH="0.700"
- KEYWORDS=""
-fi
+EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
LICENSE="GPL-2"
SLOT="0"
+KEYWORDS=""
IUSE=""
-DEPEND="dev-lang/R
+DEPEND="
+ dev-lang/R
sci-libs/htslib"
RDEPEND="${DEPEND}"
# https://github.com/ANGSD/angsd/issues/9
src_prepare(){
- sed -e 's@FLAGS=-O3@FLAGS=@' \
+ sed \
+ -e 's@FLAGS=-O3@FLAGS=@' \
+ -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+ -e 's@all: htshook angsd misc@all: angsd misc@' \
+ -i Makefile || die
+ sed \
-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
- -e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die
- sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
- -e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die
- sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die
+ -e 's@HTSDIR = .*@HTSDIR = /usr/include@' \
+ -i misc/Makefile || die
+ sed \
+ -e 's@include "../htslib/bgzf.h@include "bgzf.h@' \
+ -i misc/thetaStat.cpp || die
}
src_compile(){
@@ -45,5 +44,7 @@ src_install(){
dobin angsd
dodoc README.md
cd misc || die
- dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix
+ dobin \
+ supersim thetaStat realSFS emOptim2 msToGlf smartCount \
+ printIcounts splitgl contamination NGSadmix
}
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/angsd/metadata.xml
+++ b/sci-biology/angsd/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] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/angsd/
@ 2015-03-20 22:22 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-03-20 22:22 UTC (permalink / raw
To: gentoo-commits
commit: 80a18f092e75c49d6cd4dae6a460c197988095b7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 20 22:21:41 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 20 22:21:41 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=80a18f09
sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 version or whichever
Package-Manager: portage-2.2.15
sci-biology/angsd/ChangeLog | 10 ++++++++
sci-biology/angsd/angsd-9999.ebuild | 49 +++++++++++++++++++++++++++++++++++++
sci-biology/angsd/metadata.xml | 9 +++++++
3 files changed, 68 insertions(+)
diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog
new file mode 100644
index 0000000..a0ed763
--- /dev/null
+++ b/sci-biology/angsd/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/angsd
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*angsd-9999 (20 Mar 2015)
+
+ 20 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +angsd-9999.ebuild,
+ +metadata.xml:
+ sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700
+ version or whichever
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
new file mode 100644
index 0000000..2850ddc
--- /dev/null
+++ b/sci-biology/angsd/angsd-9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit git-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Population genetics analysis package"
+HOMEPAGE="http://www.popgen.dk/angsd"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
+ KEYWORDS=""
+else
+ EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
+ EGIT_BRANCH="0.700"
+ KEYWORDS=""
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+DEPEND="dev-lang/R
+ sci-libs/htslib"
+RDEPEND="${DEPEND}"
+
+# https://github.com/ANGSD/angsd/issues/9
+src_prepare(){
+ sed -e 's@FLAGS=-O3@FLAGS=@' \
+ -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+ -e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die
+ sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+ -e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die
+ sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die
+}
+
+src_compile(){
+ emake HTS=/usr/include
+}
+
+src_install(){
+ dobin angsd
+ dodoc README.md
+ cd misc || die
+ dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix
+}
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/angsd/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] 4+ messages in thread
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