From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 61A511396D0 for ; Sat, 2 Sep 2017 11:04:56 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9F06CE0DA7; Sat, 2 Sep 2017 11:04:55 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 6B94DE0DA7 for ; Sat, 2 Sep 2017 11:04:55 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 1167A33BEC7 for ; Sat, 2 Sep 2017 11:04:54 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id AAF308B44 for ; Sat, 2 Sep 2017 11:04:51 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1504350281.adb3bc8e64f8afe51ae31d8070b98f2a88a243ee.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/pysam/Manifest sci-biology/pysam/pysam-0.12.ebuild X-VCS-Directories: sci-biology/pysam/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: adb3bc8e64f8afe51ae31d8070b98f2a88a243ee X-VCS-Branch: master Date: Sat, 2 Sep 2017 11:04:51 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: b84cbc93-873a-42c9-887b-144f8d99045f X-Archives-Hash: 3fdc623f1e515f1526f37ba420eaacec commit: adb3bc8e64f8afe51ae31d8070b98f2a88a243ee Author: David Seifert gentoo org> AuthorDate: Sat Sep 2 10:44:42 2017 +0000 Commit: David Seifert gentoo 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 + : +}