From ce7e04bde51f3c7a2a711812dfeb991400f8baa0 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Wed, 10 Jun 2015 15:33:49 +0200 Subject: 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 0e247b8ac..cd180e7ea 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: + more comments on the external dependencies + 10 Jun 2015; Martin Mokrejs fastqc-0.11.3.ebuild: add dependency on jhdf5; more ebuild cleanup diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild index d934cae6b..7c8cb9e7b 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 Note that there is + # a newer version of this codebase at https://github.com/samtools/htsjdk but + # that FastQC is NOT yet compatible with the updated API (this will probably + # happen in a future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 } -- cgit v1.2.3-65-gdbad