[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/, profiles/
commit: 8c781c78ded4e1a70e007beb1f5b82ab863ad6cb
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 25 11:29:50 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 25 11:29:50 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c781c78
sci-biology/RSeQC: treeclean, depends on nose
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 4
sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild | 34 -
sci-biology/RSeQC/metadata.xml | 15 ---
3 files changed, 53 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index acc8c9346..a8da49349 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,7 +34,3 @@
# Needs bump of PYTHON_COMPAT to at least python3_10
sci-biology/chiron
sci-biology/trans-abyss
-
-# Andrew Ammerlaan https://sourceforge.net/projects/rseqc/;
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
- https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/nose[${PYTHON_USEDEP}]
-"
-RDEPEND="
- >=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]
- sci-biology/bx-python[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pyBigWig[${PYTHON_USEDEP}]
-"
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # avoid file collision with bx-python
- rm lib/psyco_full.py || die
-}
diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml
deleted file mode 100644
index 5c8442330..0
--- a/sci-biology/RSeQC/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- rseqc
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: c0a2ee0899f64c7262828b21e2ed793ee94d121e
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 19 09:49:20 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 19 09:49:20 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c0a2ee08
sci-biology/RSeQC: fix homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
index 4fab4c5e6..9df8930e5 100644
--- a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
@@ -8,14 +8,13 @@ PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
DESCRIPTION="Utilities for RNA-seq data quality control"
-HOMEPAGE="https://rseqc.sourceforge.net;
+HOMEPAGE="https://sourceforge.net/projects/rseqc/;
SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: 94a718a52481710ddf85e2d67ab5cd373137e3f5
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sun Jan 10 19:05:27 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sun Jan 10 19:05:27 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=94a718a5
sci-biology/RSeQC: fix file collision, bump py targets
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild | 35 +
sci-biology/RSeQC/RSeQC-4.0.0.ebuild| 28 --
2 files changed, 35 insertions(+), 28 deletions(-)
diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
new file mode 100644
index 0..4fab4c5e6
--- /dev/null
+++ b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Utilities for RNA-seq data quality control"
+HOMEPAGE="https://rseqc.sourceforge.net;
+SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
+ https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/nose[${PYTHON_USEDEP}]
+"
+RDEPEND="
+ >=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]
+ sci-biology/bx-python[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pyBigWig[${PYTHON_USEDEP}]
+"
+
+python_prepare_all() {
+ distutils-r1_python_prepare_all
+ # avoid file collision with bx-python
+ rm lib/psyco_full.py || die
+}
diff --git a/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
deleted file mode 100644
index 871aa946b..0
--- a/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Utilities for RNA-seq data quality control"
-HOMEPAGE="https://rseqc.sourceforge.net;
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
- https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
-
-# pysam (v0.7.5) was built in RSeQC. The latest version of pysam may not be
compatible with RSeQC.
-python_install(){
- distutils-r1_python_install
- rm -r "${D}$(python_get_sitedir)"/pysam
- dobin "${DISTDIR}"/fetchChromSizes
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: af893929af04f870cdb56c83d35153eb8d8d1cdc
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 18 08:32:35 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 18 08:34:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=af893929
sci-biology/RSeQC: version bump
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/RSeQC/{RSeQC-2.6.1.ebuild => RSeQC-4.0.0.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
similarity index 90%
rename from sci-biology/RSeQC/RSeQC-2.6.1.ebuild
rename to sci-biology/RSeQC/RSeQC-4.0.0.ebuild
index d3bbd9104..871aa946b 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="Utilities for RNA-seq data quality control"
HOMEPAGE="https://rseqc.sourceforge.net;
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz
+SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
LICENSE="GPL-3"
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: 801007c072e183e4abf39285ab8fd4bf290c314a Author: Horea Christian chymera eu> AuthorDate: Sat Sep 26 09:34:11 2020 + Commit: Horea Christian gmail com> CommitDate: Sat Sep 26 09:34:11 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=801007c0 sci-biology/RSeQC: PYTHON_COMPAT update Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian chymera.eu> sci-biology/RSeQC/RSeQC-2.6.1.ebuild | 12 ++-- 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild index ad9e1ce54..d3bbd9104 100644 --- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild +++ b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python3_6 ) inherit distutils-r1 DESCRIPTION="Utilities for RNA-seq data quality control" -HOMEPAGE="http://rseqc.sourceforge.net; -SRC_URI="http://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz - http://sourceforge.net/projects/rseqc/files/other/fetchChromSizes; +HOMEPAGE="https://rseqc.sourceforge.net; +SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz + https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes; LICENSE="GPL-3" SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: 8b4341068ff8fb90713bf16ed90b94d67b791563
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 24 09:25:39 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 24 09:25:39 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b434106
sci-biology/RSeQC: do not require the only tested pysam version
Package-Manager: portage-2.2.28
sci-biology/RSeQC/RSeQC-2.6.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
index 46f582b..4e3a1ff 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
@@ -18,7 +18,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]"
+DEPEND=">=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]"
RDEPEND="${DEPEND}"
# pysam (v0.7.5) was built in RSeQC. The latest version of pysam may not be
compatible with RSeQC.
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: 1f7991eb1a4e4837698ee7d5671c145dcb6d64c4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 24 09:27:17 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 24 09:27:17 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f7991eb
sci-biology/RSeQC: fix Gentoo copyright header, EAPI=6
Package-Manager: portage-2.2.28
sci-biology/RSeQC/RSeQC-2.6.1.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
index 4e3a1ff..726ec77 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
PYTHON_COMPAT=( python2_7 )
@@ -22,7 +22,6 @@ DEPEND=">=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]"
RDEPEND="${DEPEND}"
# pysam (v0.7.5) was built in RSeQC. The latest version of pysam may not be
compatible with RSeQC.
-
python_install(){
distutils-r1_python_install
rm -r "${D}$(python_get_sitedir)"/pysam
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: 33cea93a515d0fa559263ce382d76739bc4b4338
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Jun 24 14:14:54 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Jun 24 14:14:54 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=33cea93a
sci-biology/RSeQC: new package
Package-Manager: portage-2.2.18
sci-biology/RSeQC/ChangeLog | 9 +
sci-biology/RSeQC/RSeQC-2.6.1.ebuild | 30 ++
sci-biology/RSeQC/metadata.xml | 9 +
3 files changed, 48 insertions(+)
diff --git a/sci-biology/RSeQC/ChangeLog b/sci-biology/RSeQC/ChangeLog
new file mode 100644
index 000..854e7ec
--- /dev/null
+++ b/sci-biology/RSeQC/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/RSeQC
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*RSeQC-2.6.1 (24 Jun 2015)
+
+ 24 Jun 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+RSeQC-2.6.1.ebuild,
+ +metadata.xml:
+ sci-biology/RSeQC: new package
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
new file mode 100644
index 000..a6cdfed
--- /dev/null
+++ b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION=Utilities for RNA-seq data quality control
+HOMEPAGE=http://rseqc.sourceforge.net;
+SRC_URI=http://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz
+ http://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
+
+LICENSE=GPL-3
+SLOT=0
+KEYWORDS=~amd64
+IUSE=
+
+DEPEND==sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]
+RDEPEND=${DEPEND}
+
+# pysam (v0.7.5) was built in RSeQC. The latest version of pysam may not be
compatible with RSeQC.
+
+python_install(){
+ distutils-r1_python_install
+ rm -r ${D}$(python_get_sitedir)/pysam
+ dobin ${DISTDIR}/fetchChromSizes
+}
diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/RSeQC/metadata.xml
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+ herdsci-biology/herd
+ maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+ /maintainer
+/pkgmetadata
