Holger,
That particular tool uses a different loc file--all_fasta.loc, which is simply a list of fasta files with full path/name. Are your other Picard tools working? Let us know if you run into further issues.
Thanks, Kelly
On Fri Jun 24, at 7:44 AM, Holger Klein wrote:
Dear all,
I have a problem setting up the reference genomes for picard. They simply do not show up. I used revision 8c11dd28a3cf of galaxy-dist and just today switched to 720455407d1c, problem still exists.
My picard_index.loc contains the following lines: hg19full hg19 hg19 Full /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa hg18full hg18 hg18 Full /home/galaxy/galaxy-data/index_files/hg18/picard_index/hg18.fa mm9full mm9 mm9 Full /home/galaxy/galaxy-data/index_files/mm9/picard_index/mm9.fa
The respective files are also there (fa and fa.fai are links to the respective files in other dirs): /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.dict /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa.fai
Now, using e.g. the SAM/BAM Alignment Summary Metrics module from Picard, I can't choose a reference genome (no matter if it's "use assigned ref genome" or "select a different built-in genome").
It doesn't seem to be a problem of formatting or file permissions - the srma module needs the picard generated indices as well, the entries are exactly the same and there it works.
Does anyone have a hint on how to get this working?
Regards, Holger
-- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: