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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-04-20 19:05:20 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-04-20 19:05:20 +0200
commit8626e7cf15de4a26857f95608e87afdc5a18f947 (patch)
tree831baf30d8c9f29583a72a6e5bf10a30314abcf0
parentsci-biology/gffutils: version bump (diff)
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sci-biology/oncotator: new package
Package-Manager: Portage-2.3.5, Repoman-2.3.2
-rw-r--r--sci-biology/oncotator/Manifest1
-rw-r--r--sci-biology/oncotator/metadata.xml12
-rw-r--r--sci-biology/oncotator/oncotator-1.9.2.0.ebuild34
3 files changed, 47 insertions, 0 deletions
diff --git a/sci-biology/oncotator/Manifest b/sci-biology/oncotator/Manifest
new file mode 100644
index 0000000..de90530
--- /dev/null
+++ b/sci-biology/oncotator/Manifest
@@ -0,0 +1 @@
+DIST oncotator-1.9.2.0.tar.gz 12020766 SHA256 47b79c4a0cba098f0e39c10d5fc5a39bcfdd0e02689bf1f4e6ec3f04b06bd7b4 SHA512 a912081dc0d8ebf64b955e417ef88282ff2342e5e71f7edb955abc92c638acf1fd3d7bf9811909953a14639f4d3acdb6b5d522fe7bd75e9107742b1e1ed4ffcb WHIRLPOOL 3589ad6748b37447f99d803d38b2baf124afaf99c9c52e98b7e2277c5a742002d8ab10de229ce4feda85eebdf6c8be26d9799c140af10d17879b0c75457fc775
diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/oncotator/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@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
new file mode 100644
index 0000000..aa9b07b
--- /dev/null
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_5 )
+inherit distutils-r1
+
+DESCRIPTION="Annotate genetic variants in VCF"
+HOMEPAGE="https://github.com/broadinstitute/oncotator"
+SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="oncotator"
+SLOT="0"
+KEYWORDS="" # breaks silently during install because of python syntax errors
+IUSE=""
+
+DEPEND="
+ >=sci-biology/pysam-0.9.0
+ >=dev-python/bcbio-gff-0.6.2
+ >=dev-python/pyvcf-0.6.8
+ >=dev-python/pandas-0.18.0
+ >=sci-biology/biopython-1.66
+ >=dev-python/numpy-1.11.0
+ >=dev-python/cython-0.24
+ >=dev-python/shove-0.6.6
+ >=dev-python/sqlalchemy-1.0.12
+ >=dev-python/nose-1.3.7
+ >=dev-python/python-memcached-1.57
+ >=dev-python/natsort-4.0.4
+ >=dev-python/more-itertools-2.2
+ >=dev-python/enum34-1.1.2
+ dev-python/ngslib"
+RDEPEND="${DEPEND}"