Re: [galaxy-dev] Hey I got some problems using galaxy... could you help me?..
Hi, Nicola is right But I believe that your outputs aren't correctly declared. files_path keep all your files in their original directory. It's usefull when you want to build a HTML page to wrap your several outputs. In your case, I propose this command line
Re: [galaxy-dev] Variant Annotator reference genome
Hello again, My bad ! You need this : oviAri1oviAri1Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.fa A plus :) Gildas Le 10/07/2015 10:16, Sarah Maman a écrit : Hello, The Galaxy Variant Annotator tool uses this loc file : tool-data/gatk2_picard_indexes.loc This file is available in tool-data/ directory and completed but the dropdown menu of Variant Annotator tool is empty. more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1oviAri1Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai Could you please tell me where does my mistake ? Kind regards, Sarah Maman ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Variant Annotator reference genome
Hello Sarah, Check if you not use some spaces instead of tab characters in your .loc to divise your fields. Gildas Le 10/07/2015 10:16, Sarah Maman a écrit : Hello, The Galaxy Variant Annotator tool uses this loc file : tool-data/gatk2_picard_indexes.loc This file is available in tool-data/ directory and completed but the dropdown menu of Variant Annotator tool is empty. more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1oviAri1Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai Could you please tell me where does my mistake ? Kind regards, Sarah Maman ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Job still waiting - Command Line None - SGE
Not the last :/ changeset: 16054:11e14ac45c7e branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Wed Jan 21 16:00:24 2015 -0500 summary: Update tag latest_2015.01.13 for changeset 4039bfd5584a Gildas Le 30/06/2015 16:36, Alexander Vowinkel a écrit : At what galaxy version are you? 2015-06-30 7:36 GMT-05:00 Gildas Le Corguille lecorgui...@sb-roscoff.fr mailto:lecorgui...@sb-roscoff.fr: Hi, We have a problem on our production instances since one or two years (never found the time to write it and we still hope to find by ourself). Some jobs stay in waiting status (grey) indefinitely. Job ID UserLast Update ToolState Inputs Command Line Job Runner PID/Cluster ID 63094 f...@bar.fr mailto:f...@bar.fr 10 hours ago toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 new 123250 setting_metadata NoneNoneNone 63093 f...@bar.fr mailto:f...@bar.fr 10 hours ago toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 new 123249 setting_metadata NoneNoneNone 63088 f...@bar.fr mailto:f...@bar.fr 14 hours ago testtoolshed.g2.bx.psu.edu/repos/jjohnson/trinityrnaseq/trinityrnaseq_norm/0.0.2 http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/trinityrnaseq/trinityrnaseq_norm/0.0.2 new 123250 setting_metadata, 123249 setting_metadataNone NoneNone Our scheduler is SGE. We tried to found the origin of this issue : - there is not relevant clues in the log files - sometimes, a restart make start those jobs - sometimes, kill a job make the others start - sometimes, there is no choice than resubmit Is anyone can propose an idea to fix this behaviour ? Thanks Gildas ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Ideas: allow Fieldset in tool forms
Dear Galaxy Team and al., To improve the usability, it would be nice to group parameters in some kinds of fieldset. We can already hide some advanced options with conditional but ... But it's just a personal wishes And as always, great job :) Cheers Gildas ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
