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 D4E63138CDB for ; Wed, 10 Jun 2015 13:28:42 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1BBA7E083D; Wed, 10 Jun 2015 13:28:41 +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 C3DCFE07E2 for ; Wed, 10 Jun 2015 13:28:40 +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 4CDF0340C7B for ; Wed, 10 Jun 2015 13:28:39 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id CF990A2D for ; Wed, 10 Jun 2015 13:28:37 +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: <1433942862.f88203259ef0c27caa76cf104f4bf851f6e012d0.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-0.11.3.ebuild X-VCS-Directories: sci-biology/fastqc/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f88203259ef0c27caa76cf104f4bf851f6e012d0 X-VCS-Branch: master Date: Wed, 10 Jun 2015 13:28:37 +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: 80c5390c-ece4-4ec8-8a99-cfe4cd79059e X-Archives-Hash: c355de0b3b05ec885171b29f69a234f0 commit: f88203259ef0c27caa76cf104f4bf851f6e012d0 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jun 10 13:27:42 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jun 10 13:27:42 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8820325 add dependency on jhdf5; more ebuild cleanup Package-Manager: portage-2.2.18 sci-biology/fastqc/ChangeLog | 4 ++++ sci-biology/fastqc/fastqc-0.11.3.ebuild | 7 ++++--- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index 3510855..0e247b8 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Jun 2015; Martin Mokrejs + fastqc-0.11.3.ebuild: + add dependency on jhdf5; more ebuild cleanup + *fastqc-0.11.3 (30 May 2015) 30 May 2015; Martin Mokrejs diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild index d2ae40e..d934cae 100644 --- a/sci-biology/fastqc/fastqc-0.11.3.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild @@ -16,6 +16,7 @@ KEYWORDS="" IUSE="" DEPEND="sci-biology/picard + sci-libs/jhdf5 >=virtual/jre-1.5:*" RDEPEND="${DEPEND} dev-lang/perl @@ -29,7 +30,7 @@ src_prepare(){ } src_compile(){ - ant build || die # TODO: this does not work somehow + ant || die } src_install(){ @@ -38,6 +39,6 @@ src_install(){ # TODO: need to compile java in uk/ac/babraham/FastQC/ # and decide whether jbzip2-0.9.jar is a standard java lib or not - # ignore the sam-1.103.jar, that is likely library already in sci-biology/picard - # cisd-jhdf5.jar + # ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard + # cisd-jhdf5.jar should be provided by sci-libs/jhdf5 }