From cd2d3189dadad62ef240af7f543861f2f621bf4d Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Thu, 16 Nov 2017 12:39:24 +0100
Subject: [PATCH] sci-biology/HTSeq: Initial addition

Closes: https://github.com/gentoo/sci/pull/814
Package-Manager: Portage-2.3.14, Repoman-2.3.6
---
 sci-biology/HTSeq/HTSeq-0.9.1.ebuild | 31 ++++++++++++++++++++++++++++
 sci-biology/HTSeq/HTSeq-9999.ebuild  | 31 ++++++++++++++++++++++++++++
 sci-biology/HTSeq/Manifest           |  1 +
 sci-biology/HTSeq/metadata.xml       | 19 +++++++++++++++++
 4 files changed, 82 insertions(+)
 create mode 100644 sci-biology/HTSeq/HTSeq-0.9.1.ebuild
 create mode 100644 sci-biology/HTSeq/HTSeq-9999.ebuild
 create mode 100644 sci-biology/HTSeq/Manifest
 create mode 100644 sci-biology/HTSeq/metadata.xml

diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
new file mode 100644
index 000000000000..446bbef36efb
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+	${RDEPEND}
+	>=dev-lang/swig-3.0.8
+	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
new file mode 100644
index 000000000000..446bbef36efb
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+	${RDEPEND}
+	>=dev-lang/swig-3.0.8
+	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
new file mode 100644
index 000000000000..6d90d56d352f
--- /dev/null
+++ b/sci-biology/HTSeq/Manifest
@@ -0,0 +1 @@
+DIST HTSeq-0.9.1.tar.gz 596941 SHA256 af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 WHIRLPOOL da3f1d867f9cfa05e34321f75fb34ef79e943476ee650d4689e320078821703721168bfdd9e46f10f1319cc1006771cd205a80569549d21719d38aea6b0be3a8
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
new file mode 100644
index 000000000000..e9ba18c35b3c
--- /dev/null
+++ b/sci-biology/HTSeq/metadata.xml
@@ -0,0 +1,19 @@
+<?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>proxy-maint@gentoo.org</email>
+		<name>Proxy Maintainers</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">HTSeq</remote-id>
+	</upstream>
+</pkgmetadata>
-- 
2.26.2