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-rw-r--r--sci-biology/fastqc/ChangeLog4
-rw-r--r--sci-biology/fastqc/fastqc-0.11.3.ebuild15
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
@@ -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 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+ # a newer version of this codebase at https://github.com/samtools/htsjdk but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
}