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 F38421391DB for ; Sun, 23 Mar 2014 17:07:14 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 26DCBE0AC8; Sun, 23 Mar 2014 17:07:06 +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 98B7EE0AC8 for ; Sun, 23 Mar 2014 17:07:05 +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 34A7333DEE1 for ; Sun, 23 Mar 2014 17:07:04 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by spoonbill.gentoo.org (Postfix) with ESMTP id 899AD188EA for ; Sun, 23 Mar 2014 17:07:02 +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: <1395594344.0a17f05714124c90b425b51925dea9557a003422.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/fastqc/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/fastqc/ChangeLog sci-biology/fastqc/fastqc-0.10.1.ebuild sci-biology/fastqc/metadata.xml X-VCS-Directories: sci-biology/fastqc/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 0a17f05714124c90b425b51925dea9557a003422 X-VCS-Branch: master Date: Sun, 23 Mar 2014 17:07:02 +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: caebe08e-7fe5-429e-8707-14f0888db617 X-Archives-Hash: 0fece66bf4cd18e5db999eee187ed966 commit: 0a17f05714124c90b425b51925dea9557a003422 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Mar 23 17:05:44 2014 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Mar 23 17:05:44 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a17f057 sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need help Package-Manager: portage-2.2.7 --- sci-biology/fastqc/ChangeLog | 10 ++++++++++ sci-biology/fastqc/fastqc-0.10.1.ebuild | 29 +++++++++++++++++++++++++++++ sci-biology/fastqc/metadata.xml | 9 +++++++++ 3 files changed, 48 insertions(+) diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog new file mode 100644 index 0000000..69015c4 --- /dev/null +++ b/sci-biology/fastqc/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/fastqc +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*fastqc-0.10.1 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs + +fastqc-0.10.1.ebuild, +metadata.xml: + sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need + help diff --git a/sci-biology/fastqc/fastqc-0.10.1.ebuild b/sci-biology/fastqc/fastqc-0.10.1.ebuild new file mode 100644 index 0000000..5274554 --- /dev/null +++ b/sci-biology/fastqc/fastqc-0.10.1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 eutils + +DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/picard + >=virtual/jrei-1.6" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/FastQC + +src_install(){ + dobin fastqc + + # TODO: need to compile java in uk/ac/babraham/FastQC/ + # and decide whether jbzip2-0.9.jar and sam-1.32.jar are standard java libs and from samtools or whetehr not +} diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/fastqc/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +