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 18502138CDB for ; Wed, 10 Jun 2015 13:35:05 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 3F22AE07E2; Wed, 10 Jun 2015 13:35:03 +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 D98BBE07E2 for ; Wed, 10 Jun 2015 13:35:02 +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 1A4DE3409F9 for ; Wed, 10 Jun 2015 13:35:01 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B3705A0C for ; Wed, 10 Jun 2015 13:34:59 +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: <1433943229.ce7e04bde51f3c7a2a711812dfeb991400f8baa0.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: ce7e04bde51f3c7a2a711812dfeb991400f8baa0 X-VCS-Branch: master Date: Wed, 10 Jun 2015 13:34:59 +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: ecaa862a-0896-4abc-8056-b25e88428fbf X-Archives-Hash: 5c8ffb3c66323453dbf80d2deb9c148b commit: ce7e04bde51f3c7a2a711812dfeb991400f8baa0 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jun 10 13:33:49 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jun 10 13:33:49 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce7e04bd more comments on the external dependencies Package-Manager: portage-2.2.18 sci-biology/fastqc/ChangeLog | 4 ++++ sci-biology/fastqc/fastqc-0.11.3.ebuild | 15 +++++++++++++-- 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index 0e247b8..cd180e7 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -4,6 +4,10 @@ 10 Jun 2015; Martin Mokrejs fastqc-0.11.3.ebuild: + more comments on the external dependencies + + 10 Jun 2015; Martin Mokrejs + fastqc-0.11.3.ebuild: add dependency on jhdf5; more ebuild cleanup *fastqc-0.11.3 (30 May 2015) diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild index d934cae..7c8cb9e 100644 --- a/sci-biology/fastqc/fastqc-0.11.3.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild @@ -37,8 +37,19 @@ src_install(){ dobin fastqc run_fastqc.bat dodoc README.txt RELEASE_NOTES.txt - # TODO: need to compile java in uk/ac/babraham/FastQC/ - # and decide whether jbzip2-0.9.jar is a standard java lib or not + # There is no fastqc.jar. The output from the compilation is the set of + # .class files (a jar file is just a zip file full of .class files). All + # you need to copy out is the contents of the bin subdirectory, the rest of + # the download you can discard. + # + # jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2 + # # ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard + # The sam-1.103.jar library comes from + # http://sourceforge.net/projects/picard/files/sam-jdk/. Note that there is + # a newer version of this codebase at https://github.com/samtools/htsjdk but + # that FastQC is NOT yet compatible with the updated API (this will probably + # happen in a future release). This library is needed to read SAM/BAM + # format files. # cisd-jhdf5.jar should be provided by sci-libs/jhdf5 }