* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2015-06-24 14:16 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-06-24 14:16 UTC (permalink / raw
To: gentoo-commits
commit: 33cea93a515d0fa559263ce382d76739bc4b4338
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 24 14:14:54 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 24 14:14:54 2015 +0000
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 0000000..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 <mmokrejs@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 0000000..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 "${DISTDIR}"/fetchChromSizes
+}
diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/RSeQC/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2016-04-24 9:27 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-04-24 9:27 UTC (permalink / raw
To: gentoo-commits
commit: 8b4341068ff8fb90713bf16ed90b94d67b791563
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 09:25:39 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 09:25:39 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b434106
sci-biology/RSeQC: do not require the only tested pysam version
Package-Manager: portage-2.2.28
sci-biology/RSeQC/RSeQC-2.6.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
index 46f582b..4e3a1ff 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
@@ -18,7 +18,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="=sci-biology/pysam-0.7.5[${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.
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2016-04-24 9:27 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-04-24 9:27 UTC (permalink / raw
To: gentoo-commits
commit: 1f7991eb1a4e4837698ee7d5671c145dcb6d64c4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 09:27:17 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 09:27:17 2016 +0000
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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2020-09-26 9:34 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2020-09-26 9:34 UTC (permalink / raw
To: gentoo-commits
commit: 801007c072e183e4abf39285ab8fd4bf290c314a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Sep 26 09:34:11 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Sep 26 09:34:11 2020 +0000
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 <chr <AT> 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"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2020-10-18 8:34 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2020-10-18 8:34 UTC (permalink / raw
To: gentoo-commits
commit: af893929af04f870cdb56c83d35153eb8d8d1cdc
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sun Oct 18 08:32:35 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Oct 18 08:34:07 2020 +0000
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 <mmokrejs <AT> 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-${PV}.tar.gz
https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes"
LICENSE="GPL-3"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2021-01-10 19:05 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 19:05 UTC (permalink / raw
To: gentoo-commits
commit: 94a718a52481710ddf85e2d67ab5cd373137e3f5
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 19:05:27 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 19:05:27 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94a718a5
sci-biology/RSeQC: fix file collision, bump py targets
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild | 35 +++++++++++++++++++++++++++++++++
sci-biology/RSeQC/RSeQC-4.0.0.ebuild | 28 --------------------------
2 files changed, 35 insertions(+), 28 deletions(-)
diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
new file mode 100644
index 000000000..4fab4c5e6
--- /dev/null
+++ b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Utilities for RNA-seq data quality control"
+HOMEPAGE="https://rseqc.sourceforge.net"
+SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${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..000000000
--- 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
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
@ 2021-01-19 9:49 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 9:49 UTC (permalink / raw
To: gentoo-commits
commit: c0a2ee0899f64c7262828b21e2ed793ee94d121e
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 09:49:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 09:49:20 2021 +0000
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 <andrewammerlaan <AT> 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}]
^ permalink raw reply related [flat|nested] 7+ messages in thread
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