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"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

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Sarah Maman-2

"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

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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Jen Hillman-Jackson

Re: "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

Posted to: http://dev.list.galaxyproject.org/quot-Intersect-multiple-sorted-BED-files-quot-tool-data-shared-ucsc-chrom-genome-test-len-could-not-d-td4664340.html

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
-- 
          --*--
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 
         --*--
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

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The Galaxy User List is being replaced by the Galaxy Biostar
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Posts to this list will be disabled in May 2014. In the
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Jennifer Hillman-Jackson
http://galaxyproject.org