Sarah,

To my knowledge, Trackster has upgraded quite a bit since last Nov. Try upgrading and see if that helps. Be sure to see the News Brief in the link I sent for the full instructions linked in the first top section titled "Upgrades". Resetting metadata and other items may require upgrades along with the core dist repository. This was required for the Nov upgrade and can be done at any time. Will help to ensure you have fully up-to-date instance now, a good idea for troubleshooting.

Reach all News Briefs here:
https://wiki.galaxyproject.org/DevNewsBriefs

It is difficult to troubleshoot an older distribution potentially mixed with more recent changesets (these often occur in group, or have other dependencies). Starting with a stable distribution is best, especially when problems are encountered.

Our development team will send more if there additional advice. Please let us know how this works out.

Jen
Galaxy team

On 4/25/14 6:33 AM, Sarah Maman wrote:

Thanks Jennifer,

My problem is not solved yet.
The Galaxy version is not so old - November 2013 (* please see below)
len_file_path is already uncommented in universe.
Chromosome and genome are availables in loc files and tool-data/shared/ucsc/chrom also. Best, Sarah

Galaxy Version (*) :
galaxy-dev@genotoul /usr/local/bioinfo/src/galaxy-dev/galaxy-dist $ hg heads
changeset:   11219:5c789ab4144a
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Nov 04 15:04:42 2013 -0500
summary:     Added tag release_2013.11.04 for changeset 26f58e05aa10

changeset:   11216:c458a0fe1ba8
parent:      11213:6d633418ecfa
parent:      11215:f79149dd3d35
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Nov 04 14:56:57 2013 -0500
summary:     Merge security fix for filtering tools from stable/next-stable.

changeset:   11168:654dfe820960
branch:      search
parent:      11166:776ca4a63a0b
user:        Dannon Baker <dannonbaker@me.com>
date:        Fri Oct 25 15:32:18 2013 -0400
summary:     Close search branch.

changeset:   11139:7286338fd77e
branch:      extract_genomic_dna_tool_enhancements
parent:      11137:7b014440dda1
user:        John Chilton <jmchilton@gmail.com>
date:        Fri Oct 25 00:09:25 2013 -0400
summary:     Close branch extract_genomic_dna_tool_enhancements.

changeset:   11129:471f23116c5e
branch:      tool_api
parent:      11127:edab395a78b1
user:        John Chilton <jmchilton@gmail.com>
date:        Thu Oct 24 21:08:11 2013 -0500
summary:     Close branch tool_api

changeset:   11126:e19d39296919
branch:      search
parent:      11124:35a847f0f33d
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Oct 24 18:12:50 2013 -0400
summary:     Re-close search feature branch.

changeset:   11087:28d3ef3d5ed5
branch:      search
parent:      11085:f82bbdc5c22b
user:        John Chilton <jmchilton@gmail.com>
date:        Tue Oct 22 01:47:05 2013 -0500
summary:     Close branch search

changeset:   11017:c8bbd1d6c18c
branch:      api_copy_history
parent:      11015:138901353da9
user:        Carl Eberhard <carlfeberhard@gmail.com>
date:        Fri Oct 18 14:53:26 2013 -0400
summary:     Close branch: api_copy_history

changeset:   11002:acf1a0062ea8
branch:      custom-toolbox2
parent:      10997:d816d6602e18
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Oct 17 15:32:40 2013 -0400
summary:     Close feature branch for toolbox filtering 2

changeset:   10968:eeebcddfa8f4
branch:      abrenner/histogram2xml-python-module-rpy-requires-1379010965302
parent:      10964:913f3ab84629
user:        John Chilton <jmchilton@gmail.com>
date:        Thu Oct 17 04:06:42 2013 +0000
summary:     Close branch abrenner/histogram2xml-python-module-rpy-requires-1379010965302.

changeset:   10935:8b7e05aae54e
branch:      action_tpye_autoconf
parent:      10933:5a26cbd98609
user:        Dave B. <inithello@gmail.com>
date:        Tue Oct 15 15:21:52 2013 -0400
summary:     Close branch action_tpye_autoconf

changeset:   10923:914cec313725
branch:      action_tpye_make_install
parent:      10921:be307f53645c
user:        Dave Bouvier <dave@bx.psu.edu>
date:        Tue Oct 15 11:32:42 2013 -0400
summary:     Close branch action_tpye_make_install.

changeset:   10919:e3e016f0f6f3
branch:      R_environment
parent:      10917:e19c7819ea3c
user:        Dave B. <inithello@gmail.com>
date:        Tue Oct 15 11:24:21 2013 -0400
summary:     Close branch R_environment

changeset:   10913:a2b2de536a47
branch:      action_type_misc
parent:      10911:223f968a3b3c
user:        Dave B. <inithello@gmail.com>
date:        Tue Oct 15 11:15:57 2013 -0400
summary:     Close branch action_type_misc

changeset:   10612:e3e7b034cb0b
branch:      tool_api_submit
parent:      10608:abb889f8c5b7
user:        Carl Eberhard <carlfeberhard@gmail.com>
date:        Mon Sep 16 15:45:04 2013 -0400
summary:     Close branch tool_api_submit

changeset:   10564:684ef8edd1d4
branch:      dataset-cleanup
parent:      10530:e4734c99812a
user:        jeremy goecks <jeremy.goecks@emory.edu>
date:        Wed Sep 11 12:24:00 2013 -0400
summary:     Close branch 10525:e4734c99812a

changeset:   10401:53c6769dcff4
branch:      cleanup_datasets_unicode_fix
parent:      10399:b245b46ec4c0
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Aug 15 11:20:55 2013 -0400
summary:     Branch close

changeset:   10364:e68eee8054d2
branch:      sort
parent:      10362:1d91e253734e
user:        Dannon Baker <dannonbaker@me.com>
date:        Wed Aug 07 13:36:25 2013 -0400
summary:     Branch close

changeset:   10346:a849924d6f9d
branch:      extended_metadata
parent:      10343:30f0aeacf88a
user:        Dannon Baker <dannonbaker@me.com>
date:        Tue Aug 06 15:58:00 2013 -0400
summary:     Close extended_metadata branch

changeset:   10132:10810850afaa
branch:      list_published_export
parent:      10129:1d71126419b2
user:        jeremy goecks <jeremy.goecks@emory.edu>
date:        Fri Jun 21 09:27:35 2013 -0400
summary:     Close list_published_export branch

changeset:   10119:6090712e7f29
branch:      provenance
parent:      10115:471457199db2
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Jun 20 12:58:16 2013 -0400
summary:     Close provenance branch

changeset:   10114:49771dac79f2
branch:      provenance
parent:      10108:0bb601dceb65
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Jun 20 11:02:00 2013 -0400
summary:     Close provenance branch

changeset:   10091:fce9396b9a81
branch:      search
parent:      10089:fd3a82d33bb6
user:        Dannon Baker <dannonbaker@me.com>
date:        Tue Jun 18 17:22:52 2013 -0400
summary:     Close search branch

changeset:   9403:97776a49c3ed
branch:      catless-file-merge
parent:      9399:510b063792de
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Mon Apr 15 13:09:25 2013 -0400
summary:     Close catless-file-merge branch.

changeset:   9343:4e08f4804b75
branch:      error-message-fix
parent:      9336:b2a5169daea4
user:        Dannon Baker <dannonbaker@me.com>
date:        Tue Apr 09 13:25:03 2013 -0400
summary:     Close branch from Bjorn's error-message-fix pull request

changeset:   8838:499ce7fb3821
branch:      bugfixes
parent:      8835:c8b7dfb1e76d
user:        Dannon Baker <dannonbaker@me.com>
date:        Wed Feb 13 13:28:47 2013 -0500
summary:     Close branch bugfixes from PR#120

Jennifer Jackson a écrit :
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
https://wiki.galaxyproject.org/MailingLists

Galaxy Biostar is replacing the galaxy-user mailing list! Update now!
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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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          --*--
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 
         --*--

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