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
--
--*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
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