* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2015-09-24 12:56 Agostino Sarubbo
0 siblings, 0 replies; 29+ messages in thread
From: Agostino Sarubbo @ 2015-09-24 12:56 UTC (permalink / raw
To: gentoo-commits
commit: eacfdf7dded3b46636d0f4c422062216f1a6d1eb
Author: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 24 12:55:27 2015 +0000
Commit: Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Thu Sep 24 12:55:27 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eacfdf7d
sci-biology/samtools: amd64 stable wrt bug #525630
Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="amd64"
sci-biology/samtools/samtools-1.0-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild
index 802aefc..279801c 100644
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.0-r1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: 00b1d249875a5f081a74b1a248355c972b423cc3
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:30:25 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:50 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=00b1d249
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-1.0.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild
index d1f1f50..7a5f026 100644
--- a/sci-biology/samtools/samtools-1.0.ebuild
+++ b/sci-biology/samtools/samtools-1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
sci-libs/htslib"
RDEPEND="${CDEPEND}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: 31d61492a851fcda68985b29915584dda2125aa5
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:33:48 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:56 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31d61492
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-1.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild
index 3a999e0..c905fc9 100644
--- a/sci-biology/samtools/samtools-1.2.ebuild
+++ b/sci-biology/samtools/samtools-1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
>=sci-libs/htslib-${PV}"
RDEPEND="${CDEPEND}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: 92e63bcc84ec47131ccefe4f6c7dc224ff43de41
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:32:37 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:54 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92e63bcc
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-1.1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild
index 1f5b82a..235e27f 100644
--- a/sci-biology/samtools/samtools-1.1.ebuild
+++ b/sci-biology/samtools/samtools-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
~sci-libs/htslib-${PV}"
RDEPEND="${CDEPEND}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: 9de6d48e56e90183b53d6bab2e82d288a9cc0792
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:31:29 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:52 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9de6d48e
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-1.0-r1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild
index 279801c..a85053c 100644
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
sci-libs/htslib"
RDEPEND="${CDEPEND}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: 2362d04e9b57b0a3f2c2c4cc98a93fd4d52e976a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:27:22 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:45 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2362d04e
sci-biology/samtools: Trim DESCRIPTION
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-0.1.12.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild
index 34720e4..d057288 100644
--- a/sci-biology/samtools/samtools-0.1.12.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -6,7 +6,7 @@ EAPI=2
MY_P="${P}a"
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://samtools.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:40 UTC (permalink / raw
To: gentoo-commits
commit: b552f8b45630582714b2ad3df7e814eadf128acb
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:29:08 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:39:47 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b552f8b4
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-0.1.19-r2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
index 133abab..9fb708b 100644
--- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild
+++ b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://samtools.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
@@ -19,7 +19,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-CDEPEND="sys-libs/ncurses"
+CDEPEND="sys-libs/ncurses:0="
RDEPEND="${CDEPEND}
dev-lang/lua
dev-lang/perl"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-03-27 22:53 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-03-27 22:53 UTC (permalink / raw
To: gentoo-commits
commit: 5347b1b450f7d7abf30f57adaeeed3f4d6aee5d8
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 22:53:29 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 22:53:29 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5347b1b4
sci-biology/samtools: Add elog message discouraging direct use
Package-Manager: portage-2.2.28
sci-biology/samtools/samtools-0.1.20.ebuild | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild b/sci-biology/samtools/samtools-0.1.20.ebuild
index 50ee0b3..3ee9956 100644
--- a/sci-biology/samtools/samtools-0.1.20.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20.ebuild
@@ -62,3 +62,9 @@ src_install() {
use examples && dodoc -r examples
}
+
+pkg_postinst() {
+ elog "This version of samtools should *not* be your first choice for working"
+ elog "with NGS data. It is installed solely for programs requiring it."
+ elog "It is recommended that you use >=sci-biology/samtools-1.2."
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-04-09 19:58 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-04-09 19:58 UTC (permalink / raw
To: gentoo-commits
commit: 0f059b5eb7e03f75705f623dc74e27842540da40
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 9 19:58:14 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr 9 19:58:31 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f059b5e
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
.../{samtools-0.1.20-r1.ebuild => samtools-0.1.20-r2.ebuild} | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/sci-biology/samtools/samtools-0.1.20-r1.ebuild b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
similarity index 87%
rename from sci-biology/samtools/samtools-0.1.20-r1.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r2.ebuild
index 744d15f..e30ed26 100644
--- a/sci-biology/samtools/samtools-0.1.20-r1.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
@@ -20,7 +20,6 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="sys-libs/ncurses:0=
- dev-lang/lua:0
dev-lang/perl"
DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -50,6 +49,17 @@ src_install() {
mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
+ # fix perl shebangs
+ pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null
+ local i
+ for i in plot-bamcheck *.pl; do
+ sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
+ done
+
+ # remove lua scripts
+ rm -f r2plot.lua vcfutils.lua || die
+ popd >> /dev/null
+
dolib.so libbam-${SLOT}$(get_libname 1)
dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname)
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-04-10 9:21 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-04-10 9:21 UTC (permalink / raw
To: gentoo-commits
commit: 5f3acec053c0f95f355f6c4db5e12994555a4b7a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 10 09:20:56 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Apr 10 09:21:11 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f3acec0
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
.../{samtools-1.3.ebuild => samtools-1.3-r1.ebuild} | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild
similarity index 83%
rename from sci-biology/samtools/samtools-1.3.ebuild
rename to sci-biology/samtools/samtools-1.3-r1.ebuild
index ec510ec..15d6714 100644
--- a/sci-biology/samtools/samtools-1.3.ebuild
+++ b/sci-biology/samtools/samtools-1.3-r1.ebuild
@@ -20,8 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="sys-libs/ncurses:0=
- >=sci-libs/htslib-${PV}
- dev-lang/lua:0
+ =sci-libs/htslib-${PV}*
dev-lang/perl"
DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -70,7 +69,19 @@ src_test() {
src_install() {
dobin samtools $(find misc -type f -executable)
- python_replicate_script "${ED}"/usr/bin/varfilter.py
+ python_replicate_script "${ED}"usr/bin/varfilter.py
+
+ # fix perl shebangs
+ pushd "${ED}"usr/bin/ >> /dev/null
+ local i
+ for i in plot-bamstats *.pl; do
+ sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
+ done
+
+ # remove lua scripts
+ rm -f r2plot.lua vcfutils.lua || die
+ popd >> /dev/null
+
dolib.so libbam.so*
insinto /usr/include/bam
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2016-10-03 20:21 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2016-10-03 20:21 UTC (permalink / raw
To: gentoo-commits
commit: 6cd0461e803e777a0b1d91569a25a91b05edc4b1
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 3 19:50:27 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 3 20:21:21 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cd0461e
sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'
Package-Manager: portage-2.3.1
...-0.1.20-r2.ebuild => samtools-0.1.20-r3.ebuild} | 38 ++++++++++++----------
1 file changed, 21 insertions(+), 17 deletions(-)
diff --git a/sci-biology/samtools/samtools-0.1.20-r2.ebuild b/sci-biology/samtools/samtools-0.1.20-r3.ebuild
similarity index 60%
rename from sci-biology/samtools/samtools-0.1.20-r2.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r3.ebuild
index e30ed26..787add8 100644
--- a/sci-biology/samtools/samtools-0.1.20-r2.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r3.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit eutils python-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://samtools.sourceforge.net/"
@@ -16,10 +16,10 @@ LICENSE="MIT"
SLOT="0.1-legacy"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"
-
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RDEPEND="sys-libs/ncurses:0=
+RDEPEND="${PYTHON_DEPS}
+ sys-libs/ncurses:0=
dev-lang/perl"
DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -30,7 +30,8 @@ PATCHES=(
src_prepare() {
default
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+ # required, otherwise python_fix_shebang errors out
+ sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die
tc-export CC AR
}
@@ -41,24 +42,24 @@ src_compile() {
}
src_install() {
- dobin samtools $(find bcftools misc -type f -executable)
- mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die
- mkdir "${ED}"/usr/bin || die
- mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die
+ # install executables and hide them away from sight
+ dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \
+ misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
+ mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die
+ mkdir "${ED%/}"/usr/bin || die
+ mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die
- mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
- python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
+ # ... do the same with the python script, but also fix the shebang
+ mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
+ python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
# fix perl shebangs
- pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null
+ pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
local i
for i in plot-bamcheck *.pl; do
sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
done
-
- # remove lua scripts
- rm -f r2plot.lua vcfutils.lua || die
- popd >> /dev/null
+ popd >/dev/null || die
dolib.so libbam-${SLOT}$(get_libname 1)
dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname)
@@ -68,9 +69,12 @@ src_install() {
mv ${PN}{,-${SLOT}}.1 || die
doman ${PN}-${SLOT}.1
- dodoc AUTHORS NEWS
+ einstalldocs
- use examples && dodoc -r examples
+ if use examples; then
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
}
pkg_postinst() {
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2018-10-28 20:25 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2018-10-28 20:25 UTC (permalink / raw
To: gentoo-commits
commit: 18d496c1b4022e892aae9fcf3350b302b34357ed
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 28 20:24:37 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct 28 20:24:37 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18d496c1
sci-biology/samtools: Version bump to 1.9
Bug: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert <soap <AT> gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.9.ebuild | 52 ++++++++++++++++++++++++++++++++
2 files changed, 53 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 8269a052050..7ce21379a95 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
+DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9.ebuild
new file mode 100644
index 00000000000..bdcd115aafe
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.9.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools python-single-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-${PV}*
+ sys-libs/ncurses:0=
+ sys-libs/zlib:=
+ ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ python_fix_shebang misc/varfilter.py
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+
+ eautoreconf
+}
+
+src_test() {
+ local -x LD_LIBRARY_PATH="${S}"
+ default
+}
+
+src_install() {
+ default
+
+ if use examples; then
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2020-03-27 10:35 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2020-03-27 10:35 UTC (permalink / raw
To: gentoo-commits
commit: d7ff0662f30a752f5b948fda9193a27bfe09099d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 27 10:35:24 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Mar 27 10:35:24 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d7ff0662
sci-biology/samtools: Remove python dependency
Closes: https://bugs.gentoo.org/710252
Package-Manager: Portage-2.3.96, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>
.../{samtools-1.9.ebuild => samtools-1.9-r1.ebuild} | 19 ++++++++-----------
1 file changed, 8 insertions(+), 11 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9-r1.ebuild
similarity index 72%
rename from sci-biology/samtools/samtools-1.9.ebuild
rename to sci-biology/samtools/samtools-1.9-r1.ebuild
index bdcd115aafe..0d0f993895f 100644
--- a/sci-biology/samtools/samtools-1.9.ebuild
+++ b/sci-biology/samtools/samtools-1.9-r1.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools python-single-r1 toolchain-funcs
+inherit autotools toolchain-funcs
DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
@@ -15,22 +13,18 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="
dev-lang/perl
=sci-libs/htslib-${PV}*
sys-libs/ncurses:0=
- sys-libs/zlib:=
- ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
src_prepare() {
default
- python_fix_shebang misc/varfilter.py
-
# remove bundled htslib
rm -r htslib-* || die
@@ -45,6 +39,9 @@ src_test() {
src_install() {
default
+ # varfilter.py has been retired upstream for being py2 only
+ rm "${ED}"/usr/bin/varfilter.py || die
+
if use examples; then
dodoc -r examples
docompress -x /usr/share/doc/${PF}/examples
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2020-08-03 16:56 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2020-08-03 16:56 UTC (permalink / raw
To: gentoo-commits
commit: 90c55f4b6812ba59ca61467380f0a153f3ff2edf
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 16:54:23 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 16:54:23 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90c55f4b
sci-biology/samtools: Bump to version 1.10
Bug: https://bugs.gentoo.org/728018
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.10.ebuild | 56 +++++++++++++++++++++++++++++++
2 files changed, 57 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 7ce21379a95..b06f63a40e7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,4 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
+DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
diff --git a/sci-biology/samtools/samtools-1.10.ebuild b/sci-biology/samtools/samtools-1.10.ebuild
new file mode 100644
index 00000000000..0ef5e6c19e8
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.10.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-${PV}*
+ sys-libs/ncurses:0=[unicode]
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_test() {
+ # the tview test diffs expect 80-columns output
+ unset COLUMNS
+
+ default
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2020-08-03 17:40 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2020-08-03 17:40 UTC (permalink / raw
To: gentoo-commits
commit: e4e256abcf64dccd8c72ad565bd988ef49e740be
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 17:39:53 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 17:39:53 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4e256ab
sci-biology/samtools: Remove ancient py2 varfilter.py script
Closes: https://bugs.gentoo.org/735444
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
...-0.1.20-r3.ebuild => samtools-0.1.20-r4.ebuild} | 36 ++++++++--------------
1 file changed, 13 insertions(+), 23 deletions(-)
diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
similarity index 66%
rename from sci-biology/samtools/samtools-0.1.20-r3.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r4.ebuild
index 5cfcfd7f6a7..2c76f0580f8 100644
--- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1 toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://samtools.sourceforge.net/"
@@ -14,23 +12,17 @@ SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.g
LICENSE="MIT"
SLOT="0.1-legacy"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RDEPEND="${PYTHON_DEPS}
+RDEPEND="
sys-libs/ncurses:0=
dev-lang/perl"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
-PATCHES=(
- "${FILESDIR}/${P}-buildsystem.patch"
-)
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
src_prepare() {
default
- # required, otherwise python_fix_shebang errors out
- sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die
tc-export CC AR
}
@@ -48,9 +40,9 @@ src_install() {
mkdir "${ED%/}"/usr/bin || die
mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die
- # ... do the same with the python script, but also fix the shebang
- mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
- python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
+ # remove py2 script, has been removed upstream anyways
+ # https://github.com/samtools/samtools/issues/1125
+ rm "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
# fix perl shebangs
pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
@@ -70,14 +62,12 @@ src_install() {
doman ${PN}-${SLOT}.1
einstalldocs
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
}
pkg_postinst() {
elog "This version of samtools should *not* be your first choice for working"
elog "with NGS data. It is installed solely for programs requiring it."
- elog "It is recommended that you use >=sci-biology/samtools-1.2."
+ elog "It is recommended that you use >=sci-biology/samtools-1.10."
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2020-08-03 18:17 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2020-08-03 18:17 UTC (permalink / raw
To: gentoo-commits
commit: b4b33dfa42e5b47cf0bfbf07275fd5b8c576a018
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 18:17:16 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 18:17:16 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b4b33dfa
sci-biology/samtools: [QA] Fix UnnecessarySlashStrip
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/samtools-0.1.20-r4.ebuild | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/samtools/samtools-0.1.20-r4.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
index 2c76f0580f8..d598a329272 100644
--- a/sci-biology/samtools/samtools-0.1.20-r4.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
@@ -36,16 +36,16 @@ src_install() {
# install executables and hide them away from sight
dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \
misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
- mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die
- mkdir "${ED%/}"/usr/bin || die
- mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die
+ mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die
+ mkdir "${ED}"/usr/bin || die
+ mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die
# remove py2 script, has been removed upstream anyways
# https://github.com/samtools/samtools/issues/1125
- rm "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
+ rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
# fix perl shebangs
- pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
+ pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die
local i
for i in plot-bamcheck *.pl; do
sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2021-07-17 21:30 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2021-07-17 21:30 UTC (permalink / raw
To: gentoo-commits
commit: fe79f96506444e3acc34d0a971c9335026e28c7b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 17 21:30:32 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul 17 21:30:32 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fe79f965
sci-biology/samtools: Add sys-libs/ncurses[unicode(+)]
Signed-off-by: David Seifert <soap <AT> gentoo.org>
.../samtools/{samtools-1.10.ebuild => samtools-1.10-r1.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.10.ebuild b/sci-biology/samtools/samtools-1.10-r1.ebuild
similarity index 93%
rename from sci-biology/samtools/samtools-1.10.ebuild
rename to sci-biology/samtools/samtools-1.10-r1.ebuild
index 0ef5e6c19e8..94089561690 100644
--- a/sci-biology/samtools/samtools-1.10.ebuild
+++ b/sci-biology/samtools/samtools-1.10-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
RDEPEND="
dev-lang/perl
=sci-libs/htslib-${PV}*
- sys-libs/ncurses:0=[unicode]
+ sys-libs/ncurses:=[unicode(+)]
sys-libs/zlib:="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2021-10-03 17:41 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2021-10-03 17:41 UTC (permalink / raw
To: gentoo-commits
commit: e728877de767757bdff23a79092cf0fa15cf5d8a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 3 17:41:37 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct 3 17:41:37 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e728877d
sci-biology/samtools: add 1.13
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.13.ebuild | 47 +++++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 622e57502c3..2128bb6db9c 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
+DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
diff --git a/sci-biology/samtools/samtools-1.13.ebuild b/sci-biology/samtools/samtools-1.13.ebuild
new file mode 100644
index 00000000000..3165c7b7381
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.13.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-${PV}*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2021-10-11 14:55 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2021-10-11 14:55 UTC (permalink / raw
To: gentoo-commits
commit: 839c7ac1d40d861275bfb91957ce439f9502987b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 11 14:55:10 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 11 14:55:10 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=839c7ac1
sci-biology/samtools: drop 1.10-r1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 -
sci-biology/samtools/samtools-1.10-r1.ebuild | 56 ----------------------------
2 files changed, 57 deletions(-)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 2128bb6db9c..6cee5d727e1 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
diff --git a/sci-biology/samtools/samtools-1.10-r1.ebuild b/sci-biology/samtools/samtools-1.10-r1.ebuild
deleted file mode 100644
index 94089561690..00000000000
--- a/sci-biology/samtools/samtools-1.10-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-${PV}*
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-
- eautoreconf
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_test() {
- # the tview test diffs expect 80-columns output
- unset COLUMNS
-
- default
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2022-03-19 11:38 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2022-03-19 11:38 UTC (permalink / raw
To: gentoo-commits
commit: 57d20d58a279d301722f1940125c7e216249dfd5
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 11:38:04 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 11:38:04 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=57d20d58
sci-biology/samtools: add 1.15
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.15.ebuild | 47 +++++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 6cee5d727e16..d83cc15952b0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
+DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930 SHA512 21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7
diff --git a/sci-biology/samtools/samtools-1.15.ebuild b/sci-biology/samtools/samtools-1.15.ebuild
new file mode 100644
index 000000000000..74aee5acaaa2
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.15.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-${PV}*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2022-06-10 12:42 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2022-06-10 12:42 UTC (permalink / raw
To: gentoo-commits
commit: b5ba01c508dd2360e176e57e0354694dcde2616b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 10 12:41:46 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Jun 10 12:41:46 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b5ba01c5
sci-biology/samtools: add 1.15.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.15.1.ebuild | 47 +++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d83cc15952b0..a605c469e6ea 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,4 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
+DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930 SHA512 21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7
diff --git a/sci-biology/samtools/samtools-1.15.1.ebuild b/sci-biology/samtools/samtools-1.15.1.ebuild
new file mode 100644
index 000000000000..21d2b8a5077d
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.15.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-${PV}*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2022-06-19 8:09 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2022-06-19 8:09 UTC (permalink / raw
To: gentoo-commits
commit: d4b7f179a733bc6f4bc223a20f9f40825d920aa2
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 08:08:45 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 08:08:45 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d4b7f179
sci-biology/samtools: drop 1.13, 1.15
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 2 --
sci-biology/samtools/samtools-1.13.ebuild | 47 -------------------------------
sci-biology/samtools/samtools-1.15.ebuild | 47 -------------------------------
3 files changed, 96 deletions(-)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index a605c469e6ea..0ff07e0d4f83 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,4 +1,2 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
-DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930 SHA512 21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7
diff --git a/sci-biology/samtools/samtools-1.13.ebuild b/sci-biology/samtools/samtools-1.13.ebuild
deleted file mode 100644
index 3165c7b7381c..000000000000
--- a/sci-biology/samtools/samtools-1.13.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-${PV}*:=
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.15.ebuild b/sci-biology/samtools/samtools-1.15.ebuild
deleted file mode 100644
index 74aee5acaaa2..000000000000
--- a/sci-biology/samtools/samtools-1.15.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-${PV}*:=
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2022-12-27 0:06 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2022-12-27 0:06 UTC (permalink / raw
To: gentoo-commits
commit: ec7bfb77b991e596ca13696b7627f49975f8265a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 27 00:06:45 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Dec 27 00:06:45 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec7bfb77
sci-biology/samtools: add 1.16.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.16.1.ebuild | 47 +++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 0ff07e0d4f83..6836d74da51a 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
+DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild b/sci-biology/samtools/samtools-1.16.1.ebuild
new file mode 100644
index 000000000000..8047657df992
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.16.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-$(ver_cut 1-2)*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2023-02-19 15:44 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2023-02-19 15:44 UTC (permalink / raw
To: gentoo-commits
commit: 5f92906d5b563269d52f9dd1720beb098ba56edb
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 15:44:19 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 15:44:19 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f92906d
sci-biology/samtools: drop 1.15.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 -
sci-biology/samtools/samtools-1.15.1.ebuild | 47 -----------------------------
2 files changed, 48 deletions(-)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 6836d74da51a..098c93fb112b 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
diff --git a/sci-biology/samtools/samtools-1.15.1.ebuild b/sci-biology/samtools/samtools-1.15.1.ebuild
deleted file mode 100644
index 21d2b8a5077d..000000000000
--- a/sci-biology/samtools/samtools-1.15.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-${PV}*:=
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2023-03-30 11:11 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2023-03-30 11:11 UTC (permalink / raw
To: gentoo-commits
commit: 6664bbc7a20e0e9662de517ff7aced5dbc2fde9c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:10:59 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:10:59 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6664bbc7
sci-biology/samtools: add 1.17
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.17.ebuild | 47 +++++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 098c93fb112b..d6c2ed1c0762 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
+DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.17.ebuild
new file mode 100644
index 000000000000..e105621c7865
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.17.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-$(ver_cut 1-2)*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2023-04-06 19:29 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2023-04-06 19:29 UTC (permalink / raw
To: gentoo-commits
commit: d3ddf57e6ff7731bc7ceba004419cac3d6efddb1
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 6 19:29:07 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Apr 6 19:29:07 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d3ddf57e
sci-biology/samtools: drop 1.16.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 -
sci-biology/samtools/samtools-1.16.1.ebuild | 47 -----------------------------
2 files changed, 48 deletions(-)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d6c2ed1c0762..5787a3bb63e6 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild b/sci-biology/samtools/samtools-1.16.1.ebuild
deleted file mode 100644
index 8047657df992..000000000000
--- a/sci-biology/samtools/samtools-1.16.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-$(ver_cut 1-2)*:=
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2024-03-26 11:06 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2024-03-26 11:06 UTC (permalink / raw
To: gentoo-commits
commit: 0663dbd3daa9a4f9716f1238a3248e23a97767fa
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 11:06:21 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 11:06:21 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0663dbd3
sci-biology/samtools: add 1.19.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.19.2.ebuild | 47 +++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 72408c9c9544..09cffe1bb5b0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1 +1,2 @@
DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
+DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f
diff --git a/sci-biology/samtools/samtools-1.19.2.ebuild b/sci-biology/samtools/samtools-1.19.2.ebuild
new file mode 100644
index 000000000000..42879b0f8698
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.19.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-$(ver_cut 1-2)*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2024-05-24 8:59 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2024-05-24 8:59 UTC (permalink / raw
To: gentoo-commits
commit: 3e20bdaea3782bf0fcf086f01638e2731e5cda22
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri May 24 08:59:46 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri May 24 08:59:46 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e20bdae
sci-biology/samtools: drop 1.17
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 -
sci-biology/samtools/samtools-1.17.ebuild | 47 -------------------------------
2 files changed, 48 deletions(-)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 09cffe1bb5b0..3ff37ea64bc7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1 @@
-DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f
diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.17.ebuild
deleted file mode 100644
index e105621c7865..000000000000
--- a/sci-biology/samtools/samtools-1.17.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
- dev-lang/perl
- =sci-libs/htslib-$(ver_cut 1-2)*:=
- sys-libs/ncurses:=[unicode(+)]
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- default
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --with-ncurses \
- --with-htslib=system \
- CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
- emake AR="$(tc-getAR)"
-}
-
-src_install() {
- default
-
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/
@ 2024-05-24 8:59 David Seifert
0 siblings, 0 replies; 29+ messages in thread
From: David Seifert @ 2024-05-24 8:59 UTC (permalink / raw
To: gentoo-commits
commit: 6da5b3550122801911fb21b58e81be7f45d6fdce
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri May 24 08:59:50 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri May 24 08:59:50 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6da5b355
sci-biology/samtools: add 1.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/samtools/Manifest | 1 +
sci-biology/samtools/samtools-1.20.ebuild | 47 +++++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 3ff37ea64bc7..c3163dc68eeb 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1 +1,2 @@
DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f
+DIST samtools-1.20.tar.bz2 9179938 BLAKE2B b534e659899a822e191c779a6ce9247854036da3435a0b63748783edc96d610ff0f02f73bbb5c1eab3ff86dbcca331113f3312a7c3376141ef89b6a8684446e4 SHA512 8526286243d057758cb846311d0a8c728026d31438e87fcc03e0df576f33bcc6da0e18bce141dbdc438a116341c94aa92701cdf10ba6b1301eadedbb34120822
diff --git a/sci-biology/samtools/samtools-1.20.ebuild b/sci-biology/samtools/samtools-1.20.ebuild
new file mode 100644
index 000000000000..42879b0f8698
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.20.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ dev-lang/perl
+ =sci-libs/htslib-$(ver_cut 1-2)*:=
+ sys-libs/ncurses:=[unicode(+)]
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r htslib-* || die
+}
+
+src_configure() {
+ econf \
+ --with-ncurses \
+ --with-htslib=system \
+ CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
+src_install() {
+ default
+
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread
end of thread, other threads:[~2024-05-24 9:00 UTC | newest]
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