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 79414138330 for ; Fri, 26 Aug 2016 08:46:04 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 842E7E0AAA; Fri, 26 Aug 2016 08:46:01 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 0D446E0AAA for ; Fri, 26 Aug 2016 08:46:00 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B31EC340831 for ; Fri, 26 Aug 2016 08:45:58 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 1D23C245C for ; Fri, 26 Aug 2016 08:45:56 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1472200858.a58f8020918ebfc342dd2c596e4c25441bd665db.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/vcflib/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/vcflib/metadata.xml sci-biology/vcflib/vcflib-9999.ebuild X-VCS-Directories: sci-biology/vcflib/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: a58f8020918ebfc342dd2c596e4c25441bd665db X-VCS-Branch: master Date: Fri, 26 Aug 2016 08:45:56 +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: 7400aed5-fac0-4d52-ab77-b4447027441c X-Archives-Hash: d3abc16e6948a2991fcd688283e3f2db commit: a58f8020918ebfc342dd2c596e4c25441bd665db Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Aug 26 08:40:58 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Aug 26 08:40:58 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a58f8020 sci-biology/vcflib: new package, works though is not ideal Package-Manager: portage-2.3.0 sci-biology/vcflib/metadata.xml | 12 ++++++++++ sci-biology/vcflib/vcflib-9999.ebuild | 43 +++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+) diff --git a/sci-biology/vcflib/metadata.xml b/sci-biology/vcflib/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/vcflib/metadata.xml @@ -0,0 +1,12 @@ + + + + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biology@gentoo.org + Gentoo Biology Project + + diff --git a/sci-biology/vcflib/vcflib-9999.ebuild b/sci-biology/vcflib/vcflib-9999.ebuild new file mode 100644 index 0000000..5a03fe4 --- /dev/null +++ b/sci-biology/vcflib/vcflib-9999.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)" +HOMEPAGE="https://github.com/vcflib/vcflib" +EGIT_REPO_URI="https://github.com/vcflib/vcflib.git" + +# vcflib is incorporated into several projects, such as freebayes + +LICENSE="MIT-with-advertising" +SLOT="0" +KEYWORDS="" +IUSE="mpi" + +DEPEND="mpi? ( sys-cluster/openmpi )" +RDEPEND="${DEPEND}" +# contains bundled sci-biology/htslib ? +# see also ./include for possible traces of other bundled sw + +src_prepare(){ + default + sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die + sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die +} + +src_compile(){ + if use mpi ; then + emake openmp + else + emake + fi +} + +src_install(){ + dobin bin/* + dolib lib/* # install libvcflib.a + dodoc README.md +}