[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[David Seifert]

commit:     adb3bc8e64f8afe51ae31d8070b98f2a88a243ee
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 10:44:42 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 11:04:41 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=adb3bc8e

sci-biology/pysam: Bump to 0.12

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/pysam/Manifest          |  1 +
 sci-biology/pysam/pysam-0.12.ebuild | 43 +++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 24afdea8b62..b2e7af85717 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
+DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3
 DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463

diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild
new file mode 100644
index 00000000000..e181e06ac9b
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.12.ebuild
@@ -0,0 +1,43 @@
+# 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 interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.python.org/pypi/pysam"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.5*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+	export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+	# prevent setup.py from adding RPATHs
+	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+		-i cy_build.py || die
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_compile() {
+	# TODO
+	# empty compile, as the build system runs the whole build again in install
+	:
+}