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 207271391DB for ; Sun, 23 Mar 2014 21:14:56 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E213AE0C5E; Sun, 23 Mar 2014 21:14:50 +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 680D4E0C5E for ; Sun, 23 Mar 2014 21:14:50 +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 5FC9133F0F9 for ; Sun, 23 Mar 2014 21:14:49 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by spoonbill.gentoo.org (Postfix) with ESMTP id 9B6DF18875 for ; Sun, 23 Mar 2014 21:14:47 +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: <1395609219.9eb2c98e084ad39a175118774bad2e0fd587057d.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/Atlas2/Atlas2-1.4.3.ebuild sci-biology/Atlas2/ChangeLog sci-biology/Atlas2/metadata.xml X-VCS-Directories: sci-biology/Atlas2/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 9eb2c98e084ad39a175118774bad2e0fd587057d X-VCS-Branch: master Date: Sun, 23 Mar 2014 21:14:47 +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: ed3ae3f8-7b28-469f-b95c-66405b37f607 X-Archives-Hash: f1bc797c5f43c0a3e6f1af415f1ca532 commit: 9eb2c98e084ad39a175118774bad2e0fd587057d Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Mar 23 21:13:39 2014 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Mar 23 21:13:39 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9eb2c98e sci-biology/Atlas2: a skeleton for a new package, needs help from ruby team --- sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 41 ++++++++++++++++++++++++++++++++++ sci-biology/Atlas2/ChangeLog | 10 +++++++++ sci-biology/Atlas2/metadata.xml | 9 ++++++++ 3 files changed, 60 insertions(+) diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild new file mode 100644 index 0000000..7e2049d --- /dev/null +++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" + +inherit ruby-fakegem + +DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)" +HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2" +SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/ruby + sci-biology/samtools + sci-biology/blat + sci-biology/phrap + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/all/"${PN}"_v"${PV}" + +src_compile(){ + cd SOLiD-SNP-caller || die + emake + + cd ../vcfPrinter + # TODO: install the *.rb files + + cd ../Atlas-Indel2 + # TODO: install the *.rb and files in lib/ + + cd ../Atlas-SNP2 + # TODO: install +} diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog new file mode 100644 index 0000000..65bee22 --- /dev/null +++ b/sci-biology/Atlas2/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/Atlas2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Atlas2-1.4.3 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs + +Atlas2-1.4.3.ebuild, +metadata.xml: + a skeleton for a new package, needs help from ruby team + diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/Atlas2/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +