I just have symlinked the files to the right location. Is this the correct solution?

Further, I had to remove the 'chr' in the chrom len files to make it work.


Cheers,
Joachim


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 06/11/2013 03:26 PM, Joachim Jacob | VIB | wrote:
Dear all,


I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml.

Trackster displays an error after opening a saved view:

***********************
Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory
***********************

In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster
len_file_path = /mnt/referencedata/trackster

Thanks for any advice,

Cheers,
Joachim


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