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
hg18full hg18 hg18 Full
mm9full mm9 mm9 Full
The respective files are also there (fa and fa.fai are links to the
respective files in other dirs):
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?
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
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