[gentoo-commits] proj/sci:master commit in: sci-biology/seq_crumbs/

[Martin Mokrejs]

commit:     4efdba16fdc718fde4b8679fb805cb382df46fef
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr  1 15:04:25 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr  1 15:04:25 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4efdba16

sci-biology/seq_crumbs: new package

The fix to setup.py to respect DESTDIR is probably not ideal.
Needs a fix to avoid file collisions.

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/seq_crumbs/metadata.xml            | 12 +++++++
 sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild | 46 ++++++++++++++++++++++++++
 2 files changed, 58 insertions(+)

diff --git a/sci-biology/seq_crumbs/metadata.xml b/sci-biology/seq_crumbs/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/seq_crumbs/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild
new file mode 100644
index 000000000..94ce00a94
--- /dev/null
+++ b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Filter, split and trim NGS sequence data"
+HOMEPAGE="https://github.com/JoseBlanca/seq_crumbs"
+SRC_URI="https://github.com/JoseBlanca/"${PN}"/archive/v"${PV}".tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	>=sci-biology/biopython-1.60
+	>=sci-biology/pysam-0.8
+	>=dev-python/rpy-2
+	dev-python/matplotlib
+	dev-python/configobj
+	dev-python/toolz"
+RDEPEND="${DEPEND}"
+
+# TODO fix file collisions
+#  * Detected file collision(s):
+#  * 
+#  * 	/usr/share/man/man1/index.1.bz2
+#  * 	/usr/share/man/man1/install.1.bz2
+#  * 
+#  * Searching all installed packages for file collisions...
+#  * 
+#  * Press Ctrl-C to Stop
+#  * 
+#  * sys-apps/coreutils-8.29:0::gentoo
+#  * 	/usr/share/man/man1/install.1.bz2
+#  * 
+#  * media-libs/netpbm-10.76.00:0::gentoo
+#  * 	/usr/share/man/man1/index.1.bz2
+src_prepare(){
+	sed -e "s#sys.prefix#os.getenv('ED')+'/usr/'#" -i setup.py || die
+	default
+}