* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2015-03-11 19:36 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-03-11 19:36 UTC (permalink / raw
To: gentoo-commits
commit: da8f88f098f729e3f1d41ce540743453d31ab6e1
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 11 19:35:54 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 11 19:35:54 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=da8f88f0
version bump; vcftools-0.1.8-buildsystem.patch does not apply to current tree so using sed calls from within ebuild to mimic the tweaks
Package-Manager: portage-2.2.15
sci-biology/vcftools/ChangeLog | 10 ++++++
sci-biology/vcftools/metadata.xml | 5 +++
sci-biology/vcftools/vcftools-0.1.12b.ebuild | 48 ++++++++++++++++++++++++++++
3 files changed, 63 insertions(+)
diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
new file mode 100644
index 0000000..90e87e2
--- /dev/null
+++ b/sci-biology/vcftools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/vcftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vcftools-0.1.12b (11 Mar 2015)
+
+ 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +vcftools-0.1.12b.ebuild:
+ version bump; vcftools-0.1.8-buildsystem.patch does not apply to current tree
+ so using sed calls from within ebuild to mimic the tweaks
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/vcftools/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
new file mode 100644
index 0000000..bff0238
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.8.ebuild,v 1.2 2013/02/27 16:39:18 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ # epatch "${FILESDIR}"/${P}-buildsystem.patch # patch is outdated
+ sed -e 's#-O2#$(CXXFLAGS)#;s#-llapack#`$(PKG_CONFIG) --libs lapack`#' -i cpp/Makefile || die
+ tc-export CXX PKG_CONFIG
+}
+
+src_compile() {
+ local myconf
+ use lapack && myconf="VCFTOOLS_PCA=1"
+ emake -C cpp ${myconf}
+}
+
+src_install(){
+ dobin cpp/${PN}
+ insinto /usr/share/${PN}/perl
+ doins perl/*.pm
+ exeinto /usr/share/${PN}/perl
+ doexe perl/{fill,vcf}-*
+ echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}"
+ echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+ dodoc README.txt
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2015-03-19 10:37 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:37 UTC (permalink / raw
To: gentoo-commits
commit: 3db1af349c35a27a5f09fed54da8fd07b4d17664
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:35:14 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:35:14 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3db1af34
removing KEYWORDS until the perl files are installed to some other place. At the moment I get: 'perl-module.eclass: Suspicious environment values found. PERL5LIB="/usr/share/vcftools/perl"'
Package-Manager: portage-2.2.15
sci-biology/vcftools/ChangeLog | 6 ++++++
sci-biology/vcftools/vcftools-0.1.12b.ebuild | 2 +-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
index 90e87e2..a3dd0e5 100644
--- a/sci-biology/vcftools/ChangeLog
+++ b/sci-biology/vcftools/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ vcftools-0.1.12b.ebuild:
+ removing KEYWORDS until the perl files are installed to some other place. At
+ the moment I get: 'perl-module.eclass: Suspicious environment values found.
+ PERL5LIB="/usr/share/vcftools/perl"'
+
*vcftools-0.1.12b (11 Mar 2015)
11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
index bff0238..5dcac89 100644
--- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS=""
IUSE="lapack"
RDEPEND="lapack? ( virtual/lapack )"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2015-03-19 10:37 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:37 UTC (permalink / raw
To: gentoo-commits
commit: f82e0c0852e65a16c66d0a42785bc8d4609d3a9c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:35:43 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:35:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f82e0c08
EAPI bump
Package-Manager: portage-2.2.15
sci-biology/vcftools/ChangeLog | 4 ++++
sci-biology/vcftools/vcftools-0.1.12b.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
index a3dd0e5..b994b84 100644
--- a/sci-biology/vcftools/ChangeLog
+++ b/sci-biology/vcftools/ChangeLog
@@ -4,6 +4,10 @@
19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
vcftools-0.1.12b.ebuild:
+ EAPI bump
+
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ vcftools-0.1.12b.ebuild:
removing KEYWORDS until the perl files are installed to some other place. At
the moment I get: 'perl-module.eclass: Suspicious environment values found.
PERL5LIB="/usr/share/vcftools/perl"'
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
index 5dcac89..916e45f 100644
--- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.8.ebuild,v 1.2 2013/02/27 16:39:18 jlec Exp $
-EAPI=4
+EAPI=5
inherit eutils toolchain-funcs
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2015-04-16 6:34 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-04-16 6:34 UTC (permalink / raw
To: gentoo-commits
commit: 4c08c4d51d42df4ccf28aeaa23324358cb0c007b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 16 06:28:32 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 16 06:28:32 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4c08c4d5
In CVS
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/vcftools/ChangeLog | 20 ------------
sci-biology/vcftools/metadata.xml | 5 ---
sci-biology/vcftools/vcftools-0.1.12b.ebuild | 48 ----------------------------
3 files changed, 73 deletions(-)
diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
deleted file mode 100644
index b994b84..0000000
--- a/sci-biology/vcftools/ChangeLog
+++ /dev/null
@@ -1,20 +0,0 @@
-# ChangeLog for sci-biology/vcftools
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- vcftools-0.1.12b.ebuild:
- EAPI bump
-
- 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- vcftools-0.1.12b.ebuild:
- removing KEYWORDS until the perl files are installed to some other place. At
- the moment I get: 'perl-module.eclass: Suspicious environment values found.
- PERL5LIB="/usr/share/vcftools/perl"'
-
-*vcftools-0.1.12b (11 Mar 2015)
-
- 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
- +vcftools-0.1.12b.ebuild:
- version bump; vcftools-0.1.8-buildsystem.patch does not apply to current tree
- so using sed calls from within ebuild to mimic the tweaks
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
deleted file mode 100644
index 839a643..0000000
--- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE="lapack"
-
-RDEPEND="lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- # epatch "${FILESDIR}"/${P}-buildsystem.patch # patch is outdated
- sed -e 's#-O2#$(CXXFLAGS)#;s#-llapack#`$(PKG_CONFIG) --libs lapack`#' -i cpp/Makefile || die
- tc-export CXX PKG_CONFIG
-}
-
-src_compile() {
- local myconf
- use lapack && myconf="VCFTOOLS_PCA=1"
- emake -C cpp ${myconf}
-}
-
-src_install(){
- dobin cpp/${PN}
- insinto /usr/share/${PN}/perl
- doins perl/*.pm
- exeinto /usr/share/${PN}/perl
- doexe perl/{fill,vcf}-*
- echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}"
- echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}"
- doenvd "${S}/99${PN}"
- dodoc README.txt
-}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2016-10-12 6:30 Marius Brehler
0 siblings, 0 replies; 8+ messages in thread
From: Marius Brehler @ 2016-10-12 6:30 UTC (permalink / raw
To: gentoo-commits
commit: cec254823f198e90b0c51750704aab40e9e0c64c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 25 09:44:52 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Sep 25 09:44:52 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cec25482
sci-biology/vcftools: remove, in main tree
sci-biology/vcftools/metadata.xml | 11 ------
sci-biology/vcftools/vcftools-0.1.14.ebuild | 55 -----------------------------
2 files changed, 66 deletions(-)
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index 77f6f92..0000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">vcftools</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild
deleted file mode 100644
index 0e792f8..0000000
--- a/sci-biology/vcftools/vcftools-0.1.14.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs autotools
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="https://vcftools.github.io
- http://vcftools.sourceforge.net"
-SRC_URI="https://github.com/vcftools/vcftools/archive/vcftools-vcftools-v0.1.14-14-g2543f81.tar.gz"
-#SRC_URI="https://codeload.github.com/vcftools/vcftools/legacy.tar.gz/master -> ${P}.tar.gz"
-#SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="lapack"
-
-RDEPEND="lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}"/vcftools-vcftools-2543f81
-#S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- # epatch "${FILESDIR}"/${P}-buildsystem.patch
- tc-export CXX PKG_CONFIG
- eautoreconf
-}
-
-src_configure(){
- econf --enable-pca # --with-pmdir=DIR install Perl modules in DIR
-}
-
-#src_compile() {
-# local myconf
-# use lapack && myconf="VCFTOOLS_PCA=1"
-# emake -C cpp ${myconf}
-#}
-
-src_install(){
- perl_set_version
- dobin src/cpp/"${PN}"
- doman src/cpp/"${PN}".1
- insinto "${VENDOR_LIB}"
- doins src/perl/*.pm
- dobin src/perl/{fill,vcf}-*
- dodoc README.md
-}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2017-04-19 9:17 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2017-04-19 9:17 UTC (permalink / raw
To: gentoo-commits
commit: d32ee40acbcb944ebc89a37b5935e84bbe2bf36b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr 19 09:16:35 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 19 09:16:35 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d32ee40a
sci-biology/vcftools: add a pre-release version
Our build patch for 0.1.14 was accepted by upstream.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/vcftools/metadata.xml | 11 ++++++++
sci-biology/vcftools/vcftools-0.1.15_pre.ebuild | 35 +++++++++++++++++++++++++
2 files changed, 46 insertions(+)
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
new file mode 100644
index 000000000..77f6f92e0
--- /dev/null
+++ b/sci-biology/vcftools/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">vcftools</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.15_pre.ebuild b/sci-biology/vcftools/vcftools-0.1.15_pre.ebuild
new file mode 100644
index 000000000..0610b01a1
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.15_pre.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools flag-o-matic perl-functions toolchain-funcs
+
+MY_PV=${PV/_pre/}
+S="${WORKDIR}/${PN}-${MY_PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${PN}-${MY_PV}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="sys-libs/zlib
+ dev-lang/perl:=
+ lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+src_configure() {
+ perl_set_version
+
+ append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
+ append-libs $($(tc-getPKG_CONFIG) --libs lapack)
+
+ econf \
+ $(use_enable lapack pca) \
+ --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2017-07-28 20:05 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
To: gentoo-commits
commit: 58c2afe759963053ffd8e15b58f34376ea2f551f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:17:10 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=58c2afe7
sci-biology/vcftools: the 0.1.15_pre release was just renamed to 0.1.15 by upstream
Package-Manager: Portage-2.3.6, Repoman-2.3.3
.../vcftools/{vcftools-0.1.15_pre.ebuild => vcftools-0.1.15.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/vcftools/vcftools-0.1.15_pre.ebuild b/sci-biology/vcftools/vcftools-0.1.15.ebuild
similarity index 88%
rename from sci-biology/vcftools/vcftools-0.1.15_pre.ebuild
rename to sci-biology/vcftools/vcftools-0.1.15.ebuild
index a11b28325..3748c67f0 100644
--- a/sci-biology/vcftools/vcftools-0.1.15_pre.ebuild
+++ b/sci-biology/vcftools/vcftools-0.1.15.ebuild
@@ -10,7 +10,7 @@ S="${WORKDIR}/${PN}-${MY_PV}"
DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${PN}-${MY_PV}.tar.gz"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${PN}-${PV}.tar.gz"
LICENSE="LGPL-3"
SLOT="0"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 8+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
commit: 073eeef7c958c27b1446350637f65da82af168fa
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:11:06 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:11:06 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=073eeef7
sci-biology/vcftools: 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/vcftools/metadata.xml | 12 ----------
sci-biology/vcftools/vcftools-0.1.15.ebuild | 36 -----------------------------
2 files changed, 48 deletions(-)
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index 0253c16be..000000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">vcftools/vcftools</remote-id>
- <remote-id type="sourceforge">vcftools</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.15.ebuild b/sci-biology/vcftools/vcftools-0.1.15.ebuild
deleted file mode 100644
index 3748c67f0..000000000
--- a/sci-biology/vcftools/vcftools-0.1.15.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic perl-functions toolchain-funcs
-
-MY_PV=${PV/_pre/}
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${PN}-${PV}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-RDEPEND="
- sys-libs/zlib
- dev-lang/perl:=
- lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-src_configure() {
- perl_set_version
-
- append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
- append-libs $($(tc-getPKG_CONFIG) --libs lapack)
-
- econf \
- $(use_enable lapack pca) \
- --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
-}
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2017-04-19 9:17 [gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/ Martin Mokrejs
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2020-09-22 11:12 Aisha Tammy
2017-07-28 20:05 Martin Mokrejs
2016-10-12 6:30 Marius Brehler
2015-04-16 6:34 Justin Lecher
2015-03-19 10:37 Martin Mokrejs
2015-03-19 10:37 Martin Mokrejs
2015-03-11 19:36 Martin Mokrejs
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