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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-06-10 15:33:49 +0200 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-06-10 15:33:49 +0200 |
commit | ce7e04bde51f3c7a2a711812dfeb991400f8baa0 (patch) | |
tree | c59ffad9fd73cfba9e9c624465b9fb273d350516 | |
parent | add dependency on jhdf5; more ebuild cleanup (diff) | |
download | sci-ce7e04bde51f3c7a2a711812dfeb991400f8baa0.tar.gz sci-ce7e04bde51f3c7a2a711812dfeb991400f8baa0.tar.bz2 sci-ce7e04bde51f3c7a2a711812dfeb991400f8baa0.zip |
more comments on the external dependencies
Package-Manager: portage-2.2.18
-rw-r--r-- | sci-biology/fastqc/ChangeLog | 4 | ||||
-rw-r--r-- | 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 @@ -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 Note that there is + # a newer version of this codebase at https://github.com/samtools/htsjdk but + # that FastQC is NOT yet compatible with the updated API (this will probably + # happen in a future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 } |