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/
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