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 92EE8138C9D for ; Sat, 18 Apr 2015 01:02:35 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id F403FE091D; Sat, 18 Apr 2015 01:02:29 +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 89BD2E091D for ; Sat, 18 Apr 2015 01:02:29 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 17C693409AF for ; Sat, 18 Apr 2015 01:02:28 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 7339F1627D for ; Sat, 18 Apr 2015 01:02:21 +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: <1429318880.f140979d8539071c3643839bab3bd3736b42cfd5.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/cortex_var/ChangeLog sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild sci-biology/cortex_var/metadata.xml X-VCS-Directories: sci-biology/cortex_var/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f140979d8539071c3643839bab3bd3736b42cfd5 X-VCS-Branch: master Date: Sat, 18 Apr 2015 01:02:21 +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: 699972ab-bcc8-48d6-a8f5-457190b619d1 X-Archives-Hash: a052844cef3b69180dc21c6778c28985 commit: f140979d8539071c3643839bab3bd3736b42cfd5 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Apr 18 01:01:20 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Apr 18 01:01:20 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f140979d sci-biology/cortex_var: new package with bundled htslib and gsl libraries Package-Manager: portage-2.2.18 sci-biology/cortex_var/ChangeLog | 9 +++++ sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 47 +++++++++++++++++++++++ sci-biology/cortex_var/metadata.xml | 9 +++++ 3 files changed, 65 insertions(+) diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog new file mode 100644 index 0000000..7be9c85 --- /dev/null +++ b/sci-biology/cortex_var/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/cortex_var +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cortex_var-1.0.5.21 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs + +cortex_var-1.0.5.21.ebuild, +metadata.xml: + sci-biology/cortex_var: new package with bundled htslib and gsl libraries diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild new file mode 100644 index 0000000..391b45f --- /dev/null +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)" +HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" +SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz + http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://www.well.ox.ac.uk/project-stampy + +DEPEND="sci-biology/vcftools + sci-libs/gsl + sci-libs/htslib + dev-lang/perl" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/CORTEX_release_v1.0.5.21 + +src_prepare(){ + sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die +} + +src_compile(){ + rm -rf libs/htslib libs/gsl-1.15 + make NUM_COLS=1 MAXK=31 cortex_var || die +} + +src_install(){ + bash install.sh || die + perl_set_version + insinto ${VENDOR_LIB} + doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* + echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + dodoc ${DISTDIR}/cortex_var_user_manual.pdf +} diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/cortex_var/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +