[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2024-03-26 Thread David Seifert 
commit: 9e53125a7a6ae8c74dc0b154c9f14498a4bbfb0d
Author: David Seifert  gentoo  org>
AuthorDate: Tue Mar 26 11:06:22 2024 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Mar 26 11:06:22 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e53125a

sci-biology/bcftools: add 1.19

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 +
 sci-biology/bcftools/bcftools-1.19.ebuild | 42 +++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 0f3c24a476a9..9cbcbdd02db5 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 
82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502
 SHA512 
39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68
+DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 
43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f
 SHA512 
a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746

diff --git a/sci-biology/bcftools/bcftools-1.19.ebuild 
b/sci-biology/bcftools/bcftools-1.19.ebuild
new file mode 100644
index ..27d474fe35f9
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.19.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2023-04-06 Thread David Seifert 
commit: a70b50ddac48495aa2104769f34d19c007cf1861
Author: David Seifert  gentoo  org>
AuthorDate: Thu Apr  6 19:29:08 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Apr  6 19:29:08 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a70b50dd

sci-biology/bcftools: drop 1.16

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 -
 sci-biology/bcftools/bcftools-1.16.ebuild | 42 ---
 2 files changed, 43 deletions(-)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 8d5aa1eec079..0f3c24a476a9 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1 @@
-DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 
0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06
 SHA512 
998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3
 DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 
82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502
 SHA512 
39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68

diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild 
b/sci-biology/bcftools/bcftools-1.16.ebuild
deleted file mode 100644
index 6adee705bb46..
--- a/sci-biology/bcftools/bcftools-1.16.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-   =sci-libs/htslib-$(ver_cut 1-2)*:=
-   sys-libs/zlib
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --with-htslib=system
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2023-03-30 Thread David Seifert 
commit: 44c2c0b7d6006ee664863ccaf60bbde18a7a2153
Author: David Seifert  gentoo  org>
AuthorDate: Thu Mar 30 11:11:00 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Mar 30 11:11:00 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c2c0b7

sci-biology/bcftools: add 1.17

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 +
 sci-biology/bcftools/bcftools-1.17.ebuild | 42 +++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 2302cb589b4f..8d5aa1eec079 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 
0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06
 SHA512 
998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3
+DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 
82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502
 SHA512 
39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68

diff --git a/sci-biology/bcftools/bcftools-1.17.ebuild 
b/sci-biology/bcftools/bcftools-1.17.ebuild
new file mode 100644
index ..6adee705bb46
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.17.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2023-02-19 Thread David Seifert 
commit: 5cd2ddf3a6b7192026b3b80c33ba8dfcda309939
Author: David Seifert  gentoo  org>
AuthorDate: Sun Feb 19 15:44:20 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Feb 19 15:44:20 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5cd2ddf3

sci-biology/bcftools: drop 1.15.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest   |  1 -
 sci-biology/bcftools/bcftools-1.15.1.ebuild | 42 -
 2 files changed, 43 deletions(-)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index af5f3f40dd8b..2302cb589b4f 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1 @@
-DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B 
d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731
 SHA512 
60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
 DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 
0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06
 SHA512 
998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3

diff --git a/sci-biology/bcftools/bcftools-1.15.1.ebuild 
b/sci-biology/bcftools/bcftools-1.15.1.ebuild
deleted file mode 100644
index 9032b97e11d0..
--- a/sci-biology/bcftools/bcftools-1.15.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..10} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --with-htslib=system
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2022-12-26 Thread David Seifert 
commit: 01090e63f3067303d6ca41e5bbea8b890bbab7b6
Author: David Seifert  gentoo  org>
AuthorDate: Tue Dec 27 00:06:46 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Dec 27 00:06:46 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01090e63

sci-biology/bcftools: add 1.16

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 +
 sci-biology/bcftools/bcftools-1.16.ebuild | 42 +++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 4dbacdb4a399..af5f3f40dd8b 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B 
d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731
 SHA512 
60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
+DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 
0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06
 SHA512 
998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3

diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild 
b/sci-biology/bcftools/bcftools-1.16.ebuild
new file mode 100644
index ..eeb9a7c890b7
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.16.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2022-06-19 Thread David Seifert 
commit: 7b77e6902ea23156a82fa792758968421aae9342
Author: David Seifert  gentoo  org>
AuthorDate: Sun Jun 19 08:08:44 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Jun 19 08:08:44 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b77e690

sci-biology/bcftools: drop 1.13, 1.15

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  2 --
 sci-biology/bcftools/bcftools-1.13.ebuild | 44 ---
 sci-biology/bcftools/bcftools-1.15.ebuild | 44 ---
 3 files changed, 90 deletions(-)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 73403fe6ed42..4dbacdb4a399 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,3 +1 @@
-DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec7238f1e6f23a55a
 DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B 
d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731
 SHA512 
60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
-DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 
44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f
 SHA512 
43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36debdbce85161745a5a063abdbca44

diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild 
b/sci-biology/bcftools/bcftools-1.13.ebuild
deleted file mode 100644
index b0ddd23857c2..
--- a/sci-biology/bcftools/bcftools-1.13.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep '
-   dev-python/matplotlib[${PYTHON_USEDEP}]
-   ')
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --with-htslib=system
-}

diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild 
b/sci-biology/bcftools/bcftools-1.15.ebuild
deleted file mode 100644
index 4ec6b0a7e097..
--- a/sci-biology/bcftools/bcftools-1.15.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep '
-   dev-python/matplotlib[${PYTHON_USEDEP}]
-   ')
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --with-htslib=system
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2022-06-10 Thread David Seifert 
commit: 20052cf2dfdc421aa1a194bf172703dd58ebbe06
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jun 10 12:41:48 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Jun 10 12:41:48 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20052cf2

sci-biology/bcftools: add 1.15.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest   |  1 +
 sci-biology/bcftools/bcftools-1.15.1.ebuild | 42 +
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 32704684a3cf..73403fe6ed42 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1,3 @@
 DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec7238f1e6f23a55a
+DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B 
d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731
 SHA512 
60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
 DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 
44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f
 SHA512 
43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36debdbce85161745a5a063abdbca44

diff --git a/sci-biology/bcftools/bcftools-1.15.1.ebuild 
b/sci-biology/bcftools/bcftools-1.15.1.ebuild
new file mode 100644
index ..7de00114bfa6
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.15.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2022-03-19 Thread David Seifert 
commit: 65bf4360727a6bceed339106305247eb0962f654
Author: David Seifert  gentoo  org>
AuthorDate: Sat Mar 19 11:38:05 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Mar 19 11:38:05 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=65bf4360

sci-biology/bcftools: add 1.15

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 +
 sci-biology/bcftools/bcftools-1.15.ebuild | 44 +++
 2 files changed, 45 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index bfc2b78ed049..32704684a3cf 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec7238f1e6f23a55a
+DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 
44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f
 SHA512 
43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36debdbce85161745a5a063abdbca44

diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild 
b/sci-biology/bcftools/bcftools-1.15.ebuild
new file mode 100644
index ..4ec6b0a7e097
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.15.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep '
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   ')
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2021-10-11 Thread David Seifert 
commit: 0c0f7543e2f922af5b5198b2abb6d9c32b6be5cb
Author: David Seifert  gentoo  org>
AuthorDate: Mon Oct 11 14:55:09 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Oct 11 14:55:09 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c0f7543

sci-biology/bcftools: drop 1.10.2

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest   |  1 -
 sci-biology/bcftools/bcftools-1.10.2.ebuild | 43 -
 2 files changed, 44 deletions(-)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 958ce72a852..bfc2b78ed04 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1 @@
-DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 
51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e
 SHA512 
f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
 DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec7238f1e6f23a55a

diff --git a/sci-biology/bcftools/bcftools-1.10.2.ebuild 
b/sci-biology/bcftools/bcftools-1.10.2.ebuild
deleted file mode 100644
index a484f69133e..000
--- a/sci-biology/bcftools/bcftools-1.10.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep '
-   dev-python/matplotlib[${PYTHON_USEDEP}]
-   ')
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib:=
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --with-htslib=system
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2021-10-03 Thread David Seifert 
commit: 9eab85fba2bfef0ad9b849a75a7e78d2895d4eba
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct  3 17:41:38 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct  3 17:41:38 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9eab85fb

sci-biology/bcftools: add 1.13

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest |  1 +
 sci-biology/bcftools/bcftools-1.13.ebuild | 44 +++
 2 files changed, 45 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 77114df86c0..958ce72a852 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 
51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e
 SHA512 
f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
+DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec7238f1e6f23a55a

diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild 
b/sci-biology/bcftools/bcftools-1.13.ebuild
new file mode 100644
index 000..b0ddd23857c
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.13.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep '
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   ')
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/files/, sci-biology/bcftools/

2020-08-03 Thread David Seifert 
commit: 5fa92ad679d028ae8e8b88fc044bbbacd475780d
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 21:11:15 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 21:11:15 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5fa92ad6

sci-biology/bcftools: Remove old

Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest  |  2 -
 sci-biology/bcftools/bcftools-1.5.ebuild   | 45 
 sci-biology/bcftools/bcftools-1.9-r2.ebuild| 49 --
 .../bcftools/files/bcftools-1.5-buildsystem.patch  | 10 -
 .../bcftools/files/bcftools-1.5-fix-shebangs.patch | 24 ---
 .../bcftools/files/bcftools-1.9-buildsystem.patch  | 10 -
 .../bcftools/files/bcftools-1.9-fix-shebangs.patch |  8 
 7 files changed, 148 deletions(-)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 508a5c41fe3..77114df86c0 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,3 +1 @@
 DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 
51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e
 SHA512 
f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
-DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 
937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722
 SHA512 
66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
-DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B 
dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed
 SHA512 
fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c

diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild 
b/sci-biology/bcftools/bcftools-1.5.ebuild
deleted file mode 100644
index 9b5df113099..000
--- a/sci-biology/bcftools/bcftools-1.5.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-   "${FILESDIR}"/${PN}-1.5-buildsystem.patch
-   "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch
-)
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --disable-configure-htslib \
-   --with-htslib=system
-}

diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild 
b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
deleted file mode 100644
index 0963c692fcd..000
--- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6,7} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-   dev-lang/perl
-   $(python_gen_cond_dep '
-   dev-python/matplotlib[${PYTHON_MULTI_USEDEP}]
-   ')
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/zlib:=
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-   "${FILESDIR}"/${PN}-1.9-buildsystem.patch
-   "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
-)
-
-src_prepare() {
-   default
-
-   python_fix_shebang misc/{guess-ploidy,plot-roh}.py
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --disable-bcftools-plugins \
-   --disable-libgsl \
-   --disable-configure-htslib \
-   --with-htslib=system
-}

diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch 
b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
deleted file mode 100644
index 304fc03e744..000
---

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2020-08-03 Thread David Seifert 
commit: fbdda699ffc5db18d5dc0b5e2c59cf511dec93b5
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 16:54:26 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 16:54:26 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fbdda699

sci-biology/bcftools: Bump to version 1.10.2

Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/Manifest   |  1 +
 sci-biology/bcftools/bcftools-1.10.2.ebuild | 43 +
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index eef8daed7a7..508a5c41fe3 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1,3 @@
+DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 
51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e
 SHA512 
f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
 DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 
937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722
 SHA512 
66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
 DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B 
dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed
 SHA512 
fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c

diff --git a/sci-biology/bcftools/bcftools-1.10.2.ebuild 
b/sci-biology/bcftools/bcftools-1.10.2.ebuild
new file mode 100644
index 000..179f7dea77e
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.10.2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   $(python_gen_cond_dep '
+   dev-python/matplotlib[${PYTHON_MULTI_USEDEP}]
+   ')
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib:=
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --with-htslib=system
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2020-04-14 Thread Joonas Niilola 
commit: 7c72edda8eb9850fb4795352bf41eb5c2deca75c
Author: Joonas Niilola  gentoo  org>
AuthorDate: Tue Apr 14 07:58:39 2020 +
Commit: Joonas Niilola  gentoo  org>
CommitDate: Tue Apr 14 08:34:31 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7c72edda

sci-biology/bcftools: remove inactive maintainer

Signed-off-by: Joonas Niilola  gentoo.org>

 sci-biology/bcftools/metadata.xml | 4 
 1 file changed, 4 deletions(-)

diff --git a/sci-biology/bcftools/metadata.xml 
b/sci-biology/bcftools/metadata.xml
index a1fb64db6fe..0421097960c 100644
--- a/sci-biology/bcftools/metadata.xml
+++ b/sci-biology/bcftools/metadata.xml
@@ -5,10 +5,6 @@
sci-biol...@gentoo.org
Gentoo Biology Project

-   
-   mmokr...@gmail.com
-   Martin Mokrejs
-   

samtools/bcftools

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2020-03-27 Thread David Seifert 
commit: d63ea201e68952da8f5083002aedb951e4c11551
Author: David Seifert  gentoo  org>
AuthorDate: Fri Mar 27 10:35:21 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Mar 27 10:35:21 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d63ea201

sci-biology/bcftools: Add python 3.7

Package-Manager: Portage-2.3.96, Repoman-2.3.22
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/bcftools/bcftools-1.9-r2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild 
b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
index eafe63a1ee5..0963c692fcd 100644
--- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6,7} )
 
 inherit python-single-r1

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/files/, sci-biology/bcftools/

2020-02-07 Thread David Seifert 
commit: d6e49da338f6a6ce88c7bab2a4bbb643d603d95b
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Feb  7 09:42:34 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Feb  7 09:42:34 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d6e49da3

sci-biology/bcftools: fix PYTHON_COMPAT, add missing matplotlib dep

>From NEWS one can infer bcftools was at least from about 1.7 version
python3 compatible. Moreover, at the moment the shenbang lines specifically
call python3.6. So, adjust the PYTHON_COMPAT accordingly. matplotlib is
used by the python scripts, unconditionally.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Closes: https://github.com/gentoo/gentoo/pull/14421
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>
Signed-off-by: David Seifert  gentoo.org>

 .../bcftools/{bcftools-1.9.ebuild => bcftools-1.9-r1.ebuild}   |  8 
 sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch  | 10 ++
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild 
b/sci-biology/bcftools/bcftools-1.9-r1.ebuild
similarity index 84%
rename from sci-biology/bcftools/bcftools-1.9.ebuild
rename to sci-biology/bcftools/bcftools-1.9-r1.ebuild
index 53e47bc01a8..8141e6d2292 100644
--- a/sci-biology/bcftools/bcftools-1.9.ebuild
+++ b/sci-biology/bcftools/bcftools-1.9-r1.ebuild
@@ -1,9 +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 )
+PYTHON_COMPAT=( python3_6 )
 
 inherit python-single-r1
 
@@ -14,18 +14,18 @@ 
SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
dev-lang/perl
+   dev-python/matplotlib[${PYTHON_USEDEP}]
=sci-libs/htslib-${PV}*:=
sys-libs/zlib:=
${PYTHON_DEPS}"
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-   "${FILESDIR}"/${PN}-1.5-buildsystem.patch
+   "${FILESDIR}"/${PN}-1.9-buildsystem.patch
"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
 )
 

diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch 
b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
new file mode 100644
index 000..a0df4b917bc
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
@@ -0,0 +1,10 @@
+--- a/Makefile
 b/Makefile
+@@ -282,7 +282,6 @@
+   $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+   $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
+   $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
+-  $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
+ 
+ clean: testclean clean-plugins
+   -rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/files/, sci-biology/bcftools/

2018-10-28 Thread David Seifert 
commit: 59ee040ec29f25e981534026d9be99b4ca36b458
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct 28 20:24:40 2018 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct 28 20:24:40 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59ee040e

sci-biology/bcftools: Version bump to 1.9

Closes: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert  gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11

 sci-biology/bcftools/Manifest  |  1 +
 sci-biology/bcftools/bcftools-1.9.ebuild   | 47 ++
 .../bcftools/files/bcftools-1.9-fix-shebangs.patch |  8 
 3 files changed, 56 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 333bb377e49..eef8daed7a7 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 
937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722
 SHA512 
66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
+DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B 
dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed
 SHA512 
fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c

diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild 
b/sci-biology/bcftools/bcftools-1.9.ebuild
new file mode 100644
index 000..53e47bc01a8
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.9.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib:=
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+   "${FILESDIR}"/${PN}-1.5-buildsystem.patch
+   "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
+)
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/{guess-ploidy,plot-roh}.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --disable-configure-htslib \
+   --with-htslib=system
+}

diff --git a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch 
b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
new file mode 100644
index 000..76610187c49
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
@@ -0,0 +1,8 @@
+--- a/misc/vcfutils.pl
 b/misc/vcfutils.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ #
+ #   Copyright (C) 2010 Broad Institute.
+ #   Copyright (C) 2011, 2014 Genome Research Ltd.

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

2018-01-06 Thread Michał Górny 
commit: 928d19c7a4216635200a5719fcfed0ffe9d3f16f
Author: Michał Górny  gentoo  org>
AuthorDate: Sat Jan  6 10:18:06 2018 +
Commit: Michał Górny  gentoo  org>
CommitDate: Sat Jan  6 10:18:58 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=928d19c7

sci-biology/bcftools: Update contact for mmokrejs

 sci-biology/bcftools/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/bcftools/metadata.xml 
b/sci-biology/bcftools/metadata.xml
index 4fd13be2f92..a1fb64db6fe 100644
--- a/sci-biology/bcftools/metadata.xml
+++ b/sci-biology/bcftools/metadata.xml
@@ -6,7 +6,7 @@
Gentoo Biology Project


-   mmokr...@fold.natur.cuni.cz
+   mmokr...@gmail.com
Martin Mokrejs

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/, sci-biology/bcftools/files/

2017-09-02 Thread David Seifert 
commit: a26495e2ae69026f4ad9d7a730611a1cac92448e
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 12:33:32 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:35:41 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a26495e2

sci-biology/bcftools: Add 1.5 from sci overlay

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/bcftools/Manifest  |  1 +
 sci-biology/bcftools/bcftools-1.5.ebuild   | 45 ++
 .../bcftools/files/bcftools-1.5-buildsystem.patch  | 10 +
 .../bcftools/files/bcftools-1.5-fix-shebangs.patch | 24 
 sci-biology/bcftools/metadata.xml  | 15 
 5 files changed, 95 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
new file mode 100644
index 000..3540e9d20d5
--- /dev/null
+++ b/sci-biology/bcftools/Manifest
@@ -0,0 +1 @@
+DIST bcftools-1.5.tar.bz2 2975685 SHA256 
9ff75a680891467776d7064f41deb6be7a595030ba807494727cd5bee7842301 SHA512 
66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
 WHIRLPOOL 
86b827d91351d8adc026a1d851bb708e35febcc36a947532662857787ec1da6eea2c88a684b15164638b7f9235f6a6f92f4d10618e1719aa891c44c69aaece77

diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild 
b/sci-biology/bcftools/bcftools-1.5.ebuild
new file mode 100644
index 000..9b5df113099
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.5.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/zlib
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+   "${FILESDIR}"/${PN}-1.5-buildsystem.patch
+   "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch
+)
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --disable-bcftools-plugins \
+   --disable-libgsl \
+   --disable-configure-htslib \
+   --with-htslib=system
+}

diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch 
b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
new file mode 100644
index 000..304fc03e744
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
@@ -0,0 +1,10 @@
+--- a/Makefile
 b/Makefile
+@@ -275,7 +275,6 @@
+   $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+   $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
+   $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
+-  $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
+ 
+ clean: testclean clean-plugins
+   -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P

diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch 
b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch
new file mode 100644
index 000..c6cfc8b991d
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch
@@ -0,0 +1,24 @@
+--- a/misc/guess-ploidy.py
 b/misc/guess-ploidy.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python2.7
+ #
+ # Plot the output of "bcftools +guess-ploidy -v"
+ #
+--- a/misc/plot-roh.py
 b/misc/plot-roh.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python2.7
+ 
+ import glob, gzip, csv, sys, os, copy, re
+ csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
+--- a/misc/vcfutils.pl
 b/misc/vcfutils.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ #
+ #   Copyright (C) 2010 Broad Institute.
+ #   Copyright (C) 2011, 2014 Genome Research Ltd.

diff --git a/sci-biology/bcftools/metadata.xml 
b/sci-biology/bcftools/metadata.xml
new file mode 100644
index 000..4fd13be2f92
--- /dev/null
+++ b/sci-biology/bcftools/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   samtools/bcftools
+   
+