From 8626e7cf15de4a26857f95608e87afdc5a18f947 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu, 20 Apr 2017 19:05:20 +0200
Subject: sci-biology/oncotator: new package

Package-Manager: Portage-2.3.5, Repoman-2.3.2
---
 sci-biology/oncotator/Manifest                 |  1 +
 sci-biology/oncotator/metadata.xml             | 12 +++++++++
 sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 34 ++++++++++++++++++++++++++
 3 files changed, 47 insertions(+)
 create mode 100644 sci-biology/oncotator/Manifest
 create mode 100644 sci-biology/oncotator/metadata.xml
 create mode 100644 sci-biology/oncotator/oncotator-1.9.2.0.ebuild

diff --git a/sci-biology/oncotator/Manifest b/sci-biology/oncotator/Manifest
new file mode 100644
index 000000000..de90530e9
--- /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 000000000..f68a1b6fa
--- /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 000000000..aa9b07ba9
--- /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}"
-- 
cgit v1.2.3-18-g5258