1 - Pointer vers le jar GATK (derniere version : GenomeAnalysisTK-2.4-9-g532efad)

galaxy@genotoul /usr/local/bioinfo/src/galaxy/galaxy-dist $ cd
tool-data/shared/jars/
galaxy@genotoul
/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars $ ln -s
/usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar
galaxy@genotoul
/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars $ ls -ltrah
total 1,1M
-rw-r--r-- 1 galaxy wbioinfo 585K  9 sept.  2011 fastqc_v0.10.0.zip
drwxr-xr-x 9 galaxy wbioinfo  167 26 avril  2012 ..
drwxr-xr-x 6 galaxy wbioinfo  371  2 mai    2012 FastQC
lrwxrwxrwx 1 galaxy wbioinfo   44 23 juil.  2012 picard ->
/usr/local/bioinfo/src/picard-tools/current/
lrwxrwxrwx 1 galaxy wbioinfo   41 22 nov.  08:59 FindPeaks ->
/usr/local/bioinfo/src/FindPeaks/current/
lrwxrwxrwx 1 galaxy wbioinfo   40 22 nov.  11:48 ChIPMunk ->
/usr/local/bioinfo/src/ChIPMunk/current/
lrwxrwxrwx 1 galaxy wbioinfo   36 10 janv. 09:06 gatk ->
/usr/local/bioinfo/src/GATK/current/
lrwxrwxrwx 1 galaxy wbioinfo   80 23 avril 09:48 GenomeAnalysisTK.jar ->
/usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar

2 - Les 9 étapes de traitement sont regroupées en 4 modules
Module 1 = étapes 1 + 1 + 2 + 3 + 4 + 6bis
Module 2 = étapes 5 + 6
Module 3 = étapes 7 + 8 
Module 4 = étape 9

3 - Accès aux jars depuis les modules Galaxy


/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars/GenomeAnalysisTK.jar
---> ln -s /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar

/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars/AddOrReplaceReadGroups.jar
--->  $ ln -s /usr/local/bioinfo/src/picard-tools/current/AddOrReplaceReadGroups.jar


/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars/MarkDuplicates.jar
---> ln -s /usr/local/bioinfo/src/picard-tools/current/MarkDuplicates.jar


/usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars/CreateSequenceDictionary.jar
---> ln -s /usr/local/bioinfo/src/picard-tools/current/CreateSequenceDictionary.jar