* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2018-01-06 10:19 Michał Górny
0 siblings, 0 replies; 16+ messages in thread
From: Michał Górny @ 2018-01-06 10:19 UTC (permalink / raw
To: gentoo-commits
commit: 928d19c7a4216635200a5719fcfed0ffe9d3f16f
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 6 10:18:06 2018 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Jan 6 10:18:58 2018 +0000
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 @@
<name>Gentoo Biology Project</name>
</maintainer>
<maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
+ <email>mmokrejs@gmail.com</email>
<name>Martin Mokrejs</name>
</maintainer>
<upstream>
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2020-03-27 10:35 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2020-03-27 10:35 UTC (permalink / raw
To: gentoo-commits
commit: d63ea201e68952da8f5083002aedb951e4c11551
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 27 10:35:21 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Mar 27 10:35:21 2020 +0000
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 <soap <AT> 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
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2020-04-14 8:35 Joonas Niilola
0 siblings, 0 replies; 16+ messages in thread
From: Joonas Niilola @ 2020-04-14 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 7c72edda8eb9850fb4795352bf41eb5c2deca75c
Author: Joonas Niilola <juippis <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 14 07:58:39 2020 +0000
Commit: Joonas Niilola <juippis <AT> gentoo <DOT> org>
CommitDate: Tue Apr 14 08:34:31 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7c72edda
sci-biology/bcftools: remove inactive maintainer
Signed-off-by: Joonas Niilola <juippis <AT> 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 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <maintainer type="person">
- <email>mmokrejs@gmail.com</email>
- <name>Martin Mokrejs</name>
- </maintainer>
<upstream>
<remote-id type="github">samtools/bcftools</remote-id>
</upstream>
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2020-08-03 16:56 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2020-08-03 16:56 UTC (permalink / raw
To: gentoo-commits
commit: fbdda699ffc5db18d5dc0b5e2c59cf511dec93b5
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 16:54:26 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 16:54:26 2020 +0000
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 <soap <AT> 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 00000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2021-10-03 17:41 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2021-10-03 17:41 UTC (permalink / raw
To: gentoo-commits
commit: 9eab85fba2bfef0ad9b849a75a7e78d2895d4eba
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 3 17:41:38 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct 3 17:41:38 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9eab85fb
sci-biology/bcftools: add 1.13
Signed-off-by: David Seifert <soap <AT> 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 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild b/sci-biology/bcftools/bcftools-1.13.ebuild
new file mode 100644
index 00000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2021-10-11 14:55 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2021-10-11 14:55 UTC (permalink / raw
To: gentoo-commits
commit: 0c0f7543e2f922af5b5198b2abb6d9c32b6be5cb
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 11 14:55:09 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 11 14:55:09 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c0f7543
sci-biology/bcftools: drop 1.10.2
Signed-off-by: David Seifert <soap <AT> 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 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
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..00000000000
--- 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
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2022-03-19 11:38 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-03-19 11:38 UTC (permalink / raw
To: gentoo-commits
commit: 65bf4360727a6bceed339106305247eb0962f654
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 11:38:05 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 11:38:05 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=65bf4360
sci-biology/bcftools: add 1.15
Signed-off-by: David Seifert <soap <AT> 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 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
+DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f SHA512 43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44
diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild b/sci-biology/bcftools/bcftools-1.15.ebuild
new file mode 100644
index 000000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2022-06-10 12:42 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-06-10 12:42 UTC (permalink / raw
To: gentoo-commits
commit: 20052cf2dfdc421aa1a194bf172703dd58ebbe06
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 10 12:41:48 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Jun 10 12:41:48 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20052cf2
sci-biology/bcftools: add 1.15.1
Signed-off-by: David Seifert <soap <AT> 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 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
+DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f SHA512 43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44
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 000000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2022-06-19 8:09 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-06-19 8:09 UTC (permalink / raw
To: gentoo-commits
commit: 7b77e6902ea23156a82fa792758968421aae9342
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 08:08:44 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 08:08:44 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b77e690
sci-biology/bcftools: drop 1.13, 1.15
Signed-off-by: David Seifert <soap <AT> 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 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
-DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f SHA512 43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44
diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild b/sci-biology/bcftools/bcftools-1.13.ebuild
deleted file mode 100644
index b0ddd23857c2..000000000000
--- 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="${PYTHON_DEPS}"
-
-src_prepare() {
- default
-
- python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
- # remove bundled htslib
- rm -r htslib-* || die
-}
-
-src_configure() {
- econf \
- --disable-bcftools-plugins \
- --disable-libgsl \
- --with-htslib=system
-}
diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild b/sci-biology/bcftools/bcftools-1.15.ebuild
deleted file mode 100644
index 4ec6b0a7e097..000000000000
--- a/sci-biology/bcftools/bcftools-1.15.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${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
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2022-12-27 0:06 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-12-27 0:06 UTC (permalink / raw
To: gentoo-commits
commit: 01090e63f3067303d6ca41e5bbea8b890bbab7b6
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 27 00:06:46 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Dec 27 00:06:46 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01090e63
sci-biology/bcftools: add 1.16
Signed-off-by: David Seifert <soap <AT> 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 000000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2023-02-19 15:44 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-02-19 15:44 UTC (permalink / raw
To: gentoo-commits
commit: 5cd2ddf3a6b7192026b3b80c33ba8dfcda309939
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 15:44:20 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 15:44:20 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5cd2ddf3
sci-biology/bcftools: drop 1.15.1
Signed-off-by: David Seifert <soap <AT> 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..000000000000
--- 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
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2023-03-30 11:11 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-03-30 11:11 UTC (permalink / raw
To: gentoo-commits
commit: 44c2c0b7d6006ee664863ccaf60bbde18a7a2153
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:11:00 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:11:00 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c2c0b7
sci-biology/bcftools: add 1.17
Signed-off-by: David Seifert <soap <AT> 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 000000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2023-04-06 19:29 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-04-06 19:29 UTC (permalink / raw
To: gentoo-commits
commit: a70b50ddac48495aa2104769f34d19c007cf1861
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 6 19:29:08 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Apr 6 19:29:08 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a70b50dd
sci-biology/bcftools: drop 1.16
Signed-off-by: David Seifert <soap <AT> 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..000000000000
--- 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
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2024-03-26 11:06 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2024-03-26 11:06 UTC (permalink / raw
To: gentoo-commits
commit: 9e53125a7a6ae8c74dc0b154c9f14498a4bbfb0d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 11:06:22 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 11:06:22 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e53125a
sci-biology/bcftools: add 1.19
Signed-off-by: David Seifert <soap <AT> 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 000000000000..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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2024-05-24 8:59 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2024-05-24 8:59 UTC (permalink / raw
To: gentoo-commits
commit: 1af696627e09436ead88952c730660ff081c60ba
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri May 24 08:59:45 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri May 24 08:59:45 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1af69662
sci-biology/bcftools: drop 1.17
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bcftools/Manifest | 1 -
sci-biology/bcftools/bcftools-1.17.ebuild | 42 -------------------------------
2 files changed, 43 deletions(-)
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 9cbcbdd02db5..3d2a9ade06aa 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1 @@
-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-1.17.ebuild b/sci-biology/bcftools/bcftools-1.17.ebuild
deleted file mode 100644
index 6adee705bb46..000000000000
--- a/sci-biology/bcftools/bcftools-1.17.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
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/
@ 2024-05-24 8:59 David Seifert
0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2024-05-24 8:59 UTC (permalink / raw
To: gentoo-commits
commit: 4cb73988356dd75b6f43951f9e84858bac7f947f
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri May 24 08:59:51 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri May 24 08:59:51 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4cb73988
sci-biology/bcftools: add 1.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bcftools/Manifest | 1 +
sci-biology/bcftools/bcftools-1.20.ebuild | 42 +++++++++++++++++++++++++++++++
2 files changed, 43 insertions(+)
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 3d2a9ade06aa..67e4996d956c 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746
+DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17 SHA512 c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a
diff --git a/sci-biology/bcftools/bcftools-1.20.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild
new file mode 100644
index 000000000000..27d474fe35f9
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.20.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
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread
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