Hi Philippe, The GATK wrappers provided with the Galaxy distribution are for GATK version 1.4. There is a set of 1.6/GATK-lite wrappers that has been developed by the team, but is not yet available. There may also be other options available in the Tool Shed that have been contributed by the community.
Thanks for using Galaxy, Dan On Dec 11, 2012, at 5:26 PM, Philipe Moncuquet wrote: > Hi, > > I have encountered the same kind of errors. When I update the loc files link > to GATK, some of the tools display the reference genomes I added and some > not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. > GATK don't really care because they are not supporting it any more, even > documentation has disappeared. And I understand that galaxy developers have > other stuff to do than supporting a tool that will disappear because it's not > open source any more. I don't know what tool could replace the recalibration > process done by GATK and don't know how to correct bugs neither. Any > suggestions ? > > Philippe > > > > 2012/12/12 Farooq,Umar (res) <ufar...@resident.uchc.edu> > Hi, > > I am trying to incorporate GATK in my pipeline but not been able to make it > work. I aligned my data with Hg 19 and then ran sam tool filter and then > picard duplicate removal. I uploaded dbSNP and the reference FASTA file for > Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base > recalibration will not accept this output file. I wonder if there is sorting > or indexing issue but how to fix this in galaxy. > > > An error occurred running this job: Picked up _JAVA_OPTIONS: > -Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] > net.sf.picard.sam.CreateSequenceDictionary > REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta > OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp > > Thanks, > Umar > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
