[gentoo-commits] proj/sci:master commit in: sci-biology/fastqc/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     ce7e04bde51f3c7a2a711812dfeb991400f8baa0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 10 13:33:49 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 <mmokrejs@fold.natur.cuni.cz>
   fastqc-0.11.3.ebuild:
+  more comments on the external dependencies
+
+  10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  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+	# a newer version of this codebase at https://github.com/samtools/htsjdk but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
 }