From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id B2E731391DB for ; Mon, 24 Mar 2014 01:16:11 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 83100E0AB5; Mon, 24 Mar 2014 01:16:07 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 0392EE0AB5 for ; Mon, 24 Mar 2014 01:16:06 +0000 (UTC) Received: from spoonbill.gentoo.org (spoonbill.gentoo.org [81.93.255.5]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 818AC33F649 for ; Mon, 24 Mar 2014 01:16:05 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by spoonbill.gentoo.org (Postfix) with ESMTP id 2A500188EF for ; Mon, 24 Mar 2014 01:16:04 +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: <1395623696.9ce7d7d02ffa5ea884d926a61506108d5db723a5.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sga/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/sga/ChangeLog sci-biology/sga/metadata.xml sci-biology/sga/sga-9999.ebuild X-VCS-Directories: sci-biology/sga/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 9ce7d7d02ffa5ea884d926a61506108d5db723a5 X-VCS-Branch: master Date: Mon, 24 Mar 2014 01:16:04 +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: 8880a21c-23d1-49d5-ae0a-559470c52592 X-Archives-Hash: 777440cb067cb8021b3dffa1f0fc380e commit: 9ce7d7d02ffa5ea884d926a61506108d5db723a5 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Mar 24 01:14:56 2014 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 24 01:14:56 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ce7d7d0 sci-biology/sga: new package; forces its own optimization flags but works fine --- sci-biology/sga/ChangeLog | 10 +++++++++ sci-biology/sga/metadata.xml | 9 ++++++++ sci-biology/sga/sga-9999.ebuild | 47 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 66 insertions(+) diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog new file mode 100644 index 0000000..0f7e181 --- /dev/null +++ b/sci-biology/sga/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/sga +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*sga-9999 (24 Mar 2014) + + 24 Mar 2014; Martin Mokrejs +sga-9999.ebuild, + +metadata.xml: + new package; forces its own optimization flags but works fine + diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/sga/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild new file mode 100644 index 0000000..5393f87 --- /dev/null +++ b/sci-biology/sga/sga-9999.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="String Graph Assembler for short-read assemblies" +HOMEPAGE="https://github.com/jts/sga" +EGIT_REPO_URI="git://github.com/jts/sga" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="jemalloc python" + +DEPEND="dev-cpp/sparsehash + sci-biology/bamtools + sys-libs/zlib + jemalloc? ( dev-libs/jemalloc ) + python? ( sci-biology/pysam + sci-biology/ruffus )" +RDEPEND="${DEPEND}" + +src_configure(){ + cd src || die + ./autogen.sh + econf --with-bamtools=/usr +} + +src_compile(){ + cd src || die + emake +} + +src_install(){ + cd src || die + dodoc README + emake install DESTDIR="${D}" + insinto /usr/share/sga/examples + doins examples/* + cd .. || + dodoc README.md +}