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