Re: [galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
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 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 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 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 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 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 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 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 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 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 date:Thu Oct 17 04:06:42 2013 + summary: Close branch abrenner/histogram2xml-python-module-rpy-requires-1379010965302. changeset: 10935:8b7e05aae54e branch: action_tpye_autoconf parent: 10933:5a26cbd98609 user:Dave B. 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 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. 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. 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 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 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 date:Thu Aug 15 11:20:
Re: [galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
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 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 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 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 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 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 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 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 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 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 date:Thu Oct 17 04:06:42 2013 + summary: Close branch abrenner/histogram2xml-python-module-rpy-requires-1379010965302. changeset: 10935:8b7e05aae54e branch: action_tpye_autoconf parent: 10933:5a26cbd98609 user:Dave B. 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 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. 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. 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 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 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 date:Thu Aug 15 11:20:
Re: [galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
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 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 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 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 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 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 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 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 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 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 date:Thu Oct 17 04:06:42 2013 + summary: Close branch abrenner/histogram2xml-python-module-rpy-requires-1379010965302. changeset: 10935:8b7e05aae54e branch: action_tpye_autoconf parent: 10933:5a26cbd98609 user:Dave B. 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 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. 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. 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 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 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 date:Thu Aug 15 11:20:55 2013 -0400 summary: Branch close changeset: 10364:e68eee8054d2 branch: sort parent: 10362:1d91e253734e user:Dannon Baker date:Wed Aug 07 13:36:25 2013 -0400 summary: Branch close changeset: 10346:a849924d6f9d branch: extended_metadata parent: 10343:30f0aeacf88a user:Dannon Baker 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 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 date:Thu Jun 20 12:58:16 2013 -0400 summary: Close provenance branch changeset: 10114:49771dac79f2 branch: provenance parent: 10108:0bb601dceb65 user:Dannon Baker date:Thu Jun 2
[galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
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-...@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! /** ** Here's how ->>> https://wiki.galaxyproject.org/Support/Biostar** * 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 ___ Please keep all replies on the list by using "reply all" in your mail client. 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/
