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
-}
