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 9C962138A1A for ; Thu, 15 Jan 2015 17:44:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 3BE75E0828; Thu, 15 Jan 2015 17:44:24 +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 B688CE0828 for ; Thu, 15 Jan 2015 17:44:23 +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 CC2D8340683 for ; Thu, 15 Jan 2015 17:44:22 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B1B03FA44 for ; Thu, 15 Jan 2015 17:44:20 +0000 (UTC) From: "Christoph Junghans" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Christoph Junghans" Message-ID: <1421343784.806d5e4ebca3f285986f2e1e0f1125f835fdf196.ottxor@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bcftools/ChangeLog sci-biology/bcftools/bcftools-1.1.ebuild sci-biology/bcftools/metadata.xml X-VCS-Directories: sci-biology/bcftools/ X-VCS-Committer: ottxor X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: 806d5e4ebca3f285986f2e1e0f1125f835fdf196 X-VCS-Branch: master Date: Thu, 15 Jan 2015 17:44:20 +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: fbde7e9f-c3c7-4ed1-bc73-57bdd193fab3 X-Archives-Hash: fd9b70fdbb7e1f7f6a5016e1e7ade128 commit: 806d5e4ebca3f285986f2e1e0f1125f835fdf196 Author: Christoph Junghans gentoo org> AuthorDate: Thu Jan 15 17:43:04 2015 +0000 Commit: Christoph Junghans gentoo org> CommitDate: Thu Jan 15 17:43:04 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=806d5e4e Revert "Revert "sci-biology/bcftools: new package: compiles against bundled sci-libs/htslib-1.1 but does not install it"" This reverts commit 1ed8090c989cf72046e206e4daaf02222c4029a5. --- sci-biology/bcftools/ChangeLog | 10 ++++++++++ sci-biology/bcftools/bcftools-1.1.ebuild | 26 ++++++++++++++++++++++++++ sci-biology/bcftools/metadata.xml | 9 +++++++++ 3 files changed, 45 insertions(+) diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog new file mode 100644 index 0000000..4e0a781 --- /dev/null +++ b/sci-biology/bcftools/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/bcftools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*bcftools-1.1 (14 Jan 2015) + + 14 Jan 2015; Martin Mokrejs + +bcftools-1.1.ebuild, +metadata.xml: + sci-biology/bcftools: new package: compiles against bundled sci- + libs/htslib-1.1 but does not install it diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild new file mode 100644 index 0000000..e3f446f --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" +HOMEPAGE="http://www.htslib.org/bcftools_release_notes" +SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2" + +LICENSE="MIT-GRL" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sci-libs/htslib + dev-lang/perl" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e 's#prefix = /usr/local#prefix = /usr#' \ + -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall -Wc++-compat -O2@' -i Makefile + + sed -e 's#prefix = /usr/local#prefix = /usr#' \ + -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile +} diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/bcftools/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +