Hello Sarah,

This commit was made some time ago and is already in the distribution. Are you running the latest distribution?

And you have uncommented the configuration line for this in your universe.wgsi.ini file?

# Directory where chrom len files are kept, currently mainly used by trackster
#len_file_path = tool-data/shared/ucsc/chrom  <--- here

Upgrade and adjust the file as needed.
https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution

I am going to forward this over to the galaxy-dev@bx.psu.edu mailing list for further troubleshooting, should this not resolve the problem. Please keep all replies on that list.

Best,

Jen
Galaxy team
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On 4/22/14 3:25 AM, Sarah Maman wrote:
Hello,

I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (
genome_test.len in galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc fils in tool-data/) but "Intersect multiple sorted BED files" gives this error message :
An error occurred running this job: Epilog : job finished at lun. mars 24 15:55:04 CET 2014
Error: The requested genome file (/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could not be opened. Exiting!

So,
I have integrated the code modification submitted in Galaxy Central (https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2):
-                chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+                chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )

But I always have the same error message.

Could you please help us ?
Thanks in advance,
Sarah

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