* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2020-08-16 21:25 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2020-08-16 21:25 UTC (permalink / raw
To: gentoo-commits
commit: cf0b0d69d8ac7e8df14964cf9ab8b20eb224ff33
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 21:25:14 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 21:25:14 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cf0b0d69
sci-biology/bedtools: Add missing ${PYTHON_DEPS} to BDEPEND
Package-Manager: Portage-3.0.2, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/bedtools-2.29.2.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
index de337827bf2..fbc1f3a9b4f 100644
--- a/sci-biology/bedtools/bedtools-2.29.2.ebuild
+++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild
@@ -22,7 +22,9 @@ RDEPEND="
app-arch/xz-utils
sys-libs/zlib"
DEPEND="${RDEPEND}"
-BDEPEND="test? ( >=sci-biology/samtools-1.10:0 )"
+BDEPEND="
+ ${PYTHON_DEPS}
+ test? ( >=sci-biology/samtools-1.10:0 )"
S="${WORKDIR}"/${PN}2
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2022-07-08 9:09 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2022-07-08 9:09 UTC (permalink / raw
To: gentoo-commits
commit: c9aeab08ce9b02bf1d0ebb88bc599bcceb08c07b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 8 09:09:23 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Jul 8 09:09:23 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c9aeab08
sci-biology/bedtools: update EAPI 7 -> 8
Closes: https://bugs.gentoo.org/846215
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/bedtools-2.30.0.ebuild | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild
index 3647f43dabe5..3e0d51b0711b 100644
--- a/sci-biology/bedtools/bedtools-2.30.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild
@@ -1,15 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..11} )
inherit python-any-r1 toolchain-funcs
DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
HOMEPAGE="https://bedtools.readthedocs.io/"
SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+S="${WORKDIR}/${PN}2"
LICENSE="GPL-2"
SLOT="0"
@@ -26,8 +27,6 @@ BDEPEND="
${PYTHON_DEPS}
test? ( >=sci-biology/samtools-1.10:0 )"
-S="${WORKDIR}"/${PN}2
-
# bedtools2 has a *terrible* build system and development practices.
# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
# that make unbundling it nigh impossible. There are no signs of upstream porting
@@ -44,6 +43,6 @@ src_configure() {
src_install() {
default
- insinto /usr/share/${PN}
+ insinto /usr/share/bedtools
doins -r genomes
}
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2021-02-23 16:49 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2021-02-23 16:49 UTC (permalink / raw
To: gentoo-commits
commit: 3f7de88151115f14fdb6036dcffa110a0104d55b
Author: Wolfgang E. Sanyer <ezzieyguywuf <AT> gmail <DOT> com>
AuthorDate: Tue Feb 23 16:49:45 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Feb 23 16:49:45 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3f7de881
sci-biology/bedtools: bump to 2.30.0
* The samtools patch is no longer needed, as upstream has fixed this.
Test suite passes without it now.
Closes: https://github.com/gentoo/gentoo/pull/19616
Closes: https://bugs.gentoo.org/696188
Signed-off-by: Wolfgang E. Sanyer <ezzieyguywuf <AT> gmail.com>
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 1 +
sci-biology/bedtools/bedtools-2.30.0.ebuild | 49 +++++++++++++++++++++++++++++
2 files changed, 50 insertions(+)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 5dc912159a4..d2d1a7150f7 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1 +1,2 @@
DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
+DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild
new file mode 100644
index 00000000000..3647f43dabe
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+
+inherit python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/bzip2
+ app-arch/xz-utils
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ ${PYTHON_DEPS}
+ test? ( >=sci-biology/samtools-1.10:0 )"
+
+S="${WORKDIR}"/${PN}2
+
+# bedtools2 has a *terrible* build system and development practices.
+# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
+# that make unbundling it nigh impossible. There are no signs of upstream porting
+# their fork to 1.10, which means we're stuck with the bundled version.
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
+ "${FILESDIR}"/${PN}-2.29.2-python.patch
+)
+
+src_configure() {
+ tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+ default
+
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2020-08-16 20:50 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2020-08-16 20:50 UTC (permalink / raw
To: gentoo-commits
commit: e242a698ff6c378fa19286f02c735606e6a66fd6
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 20:49:52 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 20:49:52 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e242a698
sci-biology/bedtools: Remove old
Closes: https://bugs.gentoo.org/718468
Package-Manager: Portage-3.0.2, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 2 --
sci-biology/bedtools/bedtools-2.26.0.ebuild | 44 -----------------------------
2 files changed, 46 deletions(-)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index d776ef0925a..5dc912159a4 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,3 +1 @@
-DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
-DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
deleted file mode 100644
index b062a6fef84..00000000000
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit flag-o-matic python-any-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz
- https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${PYTHON_DEPS}
- test? (
- sci-libs/htslib
- sci-biology/samtools:0
- )"
-RDEPEND="sys-libs/zlib"
-
-S="${WORKDIR}/${PN}2"
-
-DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
-
-src_configure() {
- append-lfs-flags
- export prefix="${EPREFIX}/usr"
- tc-export AR CXX
-}
-
-src_install() {
- default
-
- insinto /usr/share/${PN}
- doins -r genomes
-}
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2020-04-14 8:35 Joonas Niilola
0 siblings, 0 replies; 11+ messages in thread
From: Joonas Niilola @ 2020-04-14 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 1f04dbbdbe735946dc418374152589b2ca95b26b
Author: Joonas Niilola <juippis <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 14 07:58:11 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=1f04dbbd
sci-biology/bedtools: remove inactive maintainer & long desc.
Signed-off-by: Joonas Niilola <juippis <AT> gentoo.org>
sci-biology/bedtools/metadata.xml | 11 -----------
1 file changed, 11 deletions(-)
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
index 39869a9f279..ec82800df5d 100644
--- a/sci-biology/bedtools/metadata.xml
+++ b/sci-biology/bedtools/metadata.xml
@@ -1,21 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@gmail.com</email>
- <name>Martin Mokrejs</name>
- </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <maintainer type="project">
- <email>proxy-maint@gentoo.org</email>
- <name>Proxy Maintainers</name>
- </maintainer>
- <longdescription>
- BEDTools: a flexible suite of utilities for comparing genomic features.
- </longdescription>
<upstream>
<remote-id type="google-code">bedtools</remote-id>
<remote-id type="github">arq5x/bedtools2</remote-id>
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2020-02-10 13:26 Michał Górny
0 siblings, 0 replies; 11+ messages in thread
From: Michał Górny @ 2020-02-10 13:26 UTC (permalink / raw
To: gentoo-commits
commit: cf72c05d0fba9c3ed1c9dbe63e2e1bcac1dd92ae
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 10 13:05:45 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Mon Feb 10 13:26:25 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cf72c05d
sci-biology/bedtools: Remove py2 where possible
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-biology/bedtools/bedtools-2.26.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 0ad6f3eb354..b062a6fef84 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python{2_7,3_6} )
+PYTHON_COMPAT=( python3_6 )
inherit flag-o-matic python-any-r1 toolchain-funcs
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2017-12-10 10:27 Pacho Ramos
0 siblings, 0 replies; 11+ messages in thread
From: Pacho Ramos @ 2017-12-10 10:27 UTC (permalink / raw
To: gentoo-commits
commit: 13ce867dc1600eccdb3fed302ce78265843d1980
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 10 10:21:44 2017 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Dec 10 10:21:44 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=13ce867d
sci-biology/bedtools: Add support for newer python
Package-Manager: Portage-2.3.16, Repoman-2.3.6
sci-biology/bedtools/bedtools-2.26.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 0520143f3d9..084192dd441 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
inherit flag-o-matic python-any-r1 toolchain-funcs
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2016-11-27 12:43 Pacho Ramos
0 siblings, 0 replies; 11+ messages in thread
From: Pacho Ramos @ 2016-11-27 12:43 UTC (permalink / raw
To: gentoo-commits
commit: 20fe6fef605ee8b42405629bcef94fe24f158c21
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 27 12:37:49 2016 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Nov 27 12:43:47 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20fe6fef
sci-biology/bedtools: This needs slot 0 of samtools (#597982)
Package-Manager: portage-2.3.2
sci-biology/bedtools/bedtools-2.26.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index a4c1266..04e69fb 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -20,7 +20,7 @@ IUSE="test"
DEPEND="${PYTHON_DEPS}
test? (
sci-libs/htslib
- sci-biology/samtools
+ sci-biology/samtools:0
)"
RDEPEND="sys-libs/zlib"
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2016-09-24 23:12 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2016-09-24 23:12 UTC (permalink / raw
To: gentoo-commits
commit: 566e3ceb401d95f67a2c31933b547ecd4646d48f
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 23:12:20 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 23:12:20 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=566e3ceb
sci-biology/bedtools: Add missing RDEPEND on sys-libs/zlib
Package-Manager: portage-2.3.1
sci-biology/bedtools/bedtools-2.26.0.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index feddd87..a4c1266 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -22,6 +22,7 @@ DEPEND="${PYTHON_DEPS}
sci-libs/htslib
sci-biology/samtools
)"
+RDEPEND="sys-libs/zlib"
S="${WORKDIR}/${PN}2"
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2016-09-24 22:55 David Seifert
0 siblings, 0 replies; 11+ messages in thread
From: David Seifert @ 2016-09-24 22:55 UTC (permalink / raw
To: gentoo-commits
commit: 8f2c0bf2f444a049e647bc49788ff9ae9f57b9e9
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 22:48:54 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 22:55:41 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8f2c0bf2
sci-biology/bedtools: Remove old ebuilds
Package-Manager: portage-2.3.1
sci-biology/bedtools/Manifest | 2 --
sci-biology/bedtools/bedtools-2.16.2.ebuild | 33 -----------------------------
sci-biology/bedtools/bedtools-2.20.1.ebuild | 33 -----------------------------
3 files changed, 68 deletions(-)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index c5daa59..e398b3b 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,3 +1 @@
-DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 SHA512 4dfeb048a7eacb1ca70caed64087d279aa955f30cf685f938e5a02ba328d1a878a75bfe37b537fc06cf9023474e4922719f1b391943ff0143c7760e987fa4645 WHIRLPOOL d6b89fdd4dc1f7bebcda71ea7b4c76c5d5811d7b23861019e19667171572743bd8dfbd74d4e80838aa4bfa06a524bcfaf5e76cd52c49b0658929b0060ee3aaa0
-DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84
DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2
diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild
deleted file mode 100644
index 3920b48..00000000
--- a/sci-biology/bedtools/bedtools-2.16.2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit flag-o-matic
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="https://github.com/arq5x/bedtools2"
-SRC_URI="https://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/BEDTools-Version-${PV}"
-
-src_prepare() {
- filter-ldflags -Wl,--as-needed
- sed -i \
- -e '/export CXXFLAGS/ d' \
- -e '/export CXX/ d' \
- Makefile || die
-}
-
-src_install() {
- dobin bin/*
- dodoc README* RELEASE_HISTORY
- insinto /usr/share/${PN}
- doins -r genomes
-}
diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild
deleted file mode 100644
index 2e1acbc..00000000
--- a/sci-biology/bedtools/bedtools-2.20.1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit flag-o-matic
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="https://github.com/arq5x/bedtools2"
-SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/bedtools2-${PV}"
-
-src_prepare() {
- filter-ldflags -Wl,--as-needed
- sed -i \
- -e '/export CXXFLAGS/ d' \
- -e '/export CXX/ d' \
- Makefile || die
-}
-
-src_install() {
- dobin bin/*
- dodoc README* RELEASE_HISTORY
- insinto /usr/share/${PN}
- doins -r genomes
-}
^ permalink raw reply related [flat|nested] 11+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/
@ 2015-09-01 20:06 Tobias Klausmann
0 siblings, 0 replies; 11+ messages in thread
From: Tobias Klausmann @ 2015-09-01 20:06 UTC (permalink / raw
To: gentoo-commits
commit: 6b6bd3af0034a2360cf0085a13e4d3d560639fc8
Author: Tobias Klausmann <klausman <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 1 19:57:29 2015 +0000
Commit: Tobias Klausmann <klausman <AT> gentoo <DOT> org>
CommitDate: Tue Sep 1 19:57:29 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6b6bd3af
sci-biology/bedtools: Fixing HOMEPAGE move due to code.google.com shutdown
Package-Manager: portage-2.2.20.1
sci-biology/bedtools/bedtools-2.16.2.ebuild | 2 +-
sci-biology/bedtools/bedtools-2.20.1.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild
index 9a8fdda..3920b48 100644
--- a/sci-biology/bedtools/bedtools-2.16.2.ebuild
+++ b/sci-biology/bedtools/bedtools-2.16.2.ebuild
@@ -7,7 +7,7 @@ EAPI=4
inherit flag-o-matic
DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="https://code.google.com/p/bedtools/"
+HOMEPAGE="https://github.com/arq5x/bedtools2"
SRC_URI="https://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
LICENSE="GPL-2"
diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild
index 637ce63..2e1acbc 100644
--- a/sci-biology/bedtools/bedtools-2.20.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.20.1.ebuild
@@ -7,7 +7,7 @@ EAPI=4
inherit flag-o-matic
DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="https://code.google.com/p/bedtools/"
+HOMEPAGE="https://github.com/arq5x/bedtools2"
SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
LICENSE="GPL-2"
^ permalink raw reply related [flat|nested] 11+ messages in thread
end of thread, other threads:[~2022-07-08 9:09 UTC | newest]
Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2020-08-16 21:25 [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/ David Seifert
-- strict thread matches above, loose matches on Subject: below --
2022-07-08 9:09 David Seifert
2021-02-23 16:49 David Seifert
2020-08-16 20:50 David Seifert
2020-04-14 8:35 Joonas Niilola
2020-02-10 13:26 Michał Górny
2017-12-10 10:27 Pacho Ramos
2016-11-27 12:43 Pacho Ramos
2016-09-24 23:12 David Seifert
2016-09-24 22:55 David Seifert
2015-09-01 20:06 Tobias Klausmann
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox