Posted to: http://dev.list.galaxyproject.org/quot-Intersect-multiple-sorted-BED-files-q...

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/7105c53139d4b8649e6a3714...):

•            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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