Re: [galaxy-dev] use multiple cores in BWA
On Thursday, November 29, 2012, Fenglou Mao wrote: I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried Full Parameter List, anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank The number of cores isn't exposed to the end user (although in some cases it might make sense to do so), but is rather down to the Galaxy administrators (in some cases by editing the defaults in the tool XML or wrapper scripts). There was a discussion about this on the list recently. Peter ___ 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/
Re: [galaxy-dev] Which version of GATK work with Galaxy?
On 11/29/2012 11:09 PM, Fenglou Mao wrote: When I use an old version of GATK, it failed with a report -nt option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report -et NO_ET need a key file to work since new GATK force users to report usage unless we obtain a key file, but it seems no place for galaxy to specify the key file. We are using GATK 1.4 with success. ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTK-1.4.tar.bz2 Hope this helps, Mauro Any help? Thanks, Frank ___ 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/ -- Mauro ___ 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/
Re: [galaxy-dev] Data/history/user export and import
Jeremy Thanks for the reply and the card :-) Didn't know if it was there or not so that's why the crosspost. I was thinking whether I could establish the same from using the DB access directly!? Or would that be too dangerous? In the past I have tried to transfer the user tables from an old instance into a fresh onebut failed due to all sorts of unpredictable errors.. Alex -Oorspronkelijk bericht- Van: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Verzonden: donderdag 29 november 2012 17:35 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Galaxy-dev Onderwerp: Re: [galaxy-dev] Data/history/user export and import (New feature discussion belong on the -dev list.) This is not possible now but is pretty simple to do in the future: (a) abstract the import/export history functionality into the UsesHistoryMixin; and (b) make import/export available via the API. I've made a Trello card for this: https://trello.com/c/qhu1KdWU Best, J. On Nov 29, 2012, at 8:36 AM, Bossers, Alex wrote: Dear all, Would it be possible somehow to not only export a single history of a user (to file) but also all histories of a user in one go. Or even all user-bound histories/settings and such? I would like to import them into another galaxy instance (basically from our internal development (galaxy_central) server to our public production (galaxy-dist) server), but going over them one-by-one will be a laborious task. Both instances are up-to-date. I do have admin access to both the galaxy instances (as we own them) so admin bound tools and/or possibilities from commandline would be suitable as well. Since I am unsure where it fits in the user-list or dev-list I cross-posted to both (sorry). Thanks in advance! Alex ___ 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/ ___ 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/
[galaxy-dev] Workflow loading problem
Hi, I have imported a workflow to my local Galaxy with unrecognised tools. When I try to edit this workflow it will not load. I now realise I have the same problem with some existing workflows where a tool has been removed from Galaxy, I would like to replace these workflow steps without creating a new workflow. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/
Re: [galaxy-dev] Changing interface design
Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location. Changes might only be visible when restarting the instance though! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Philipe Moncuquet Verzonden: vrijdag 30 november 2012 5:11 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Changing interface design Hi I am not satisfied with some colors of the interface. I am color blind and it's hard to discriminate between job running (light yellow) and job done (light green). Well most of the time I focus on red jobs right but anyway I would like to be able to change these stuff. Can anybody point me the file I am supposed to modify to be able to do so. Many thanks in advance. Philippe ___ 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/
Re: [galaxy-dev] Changing interface design
Hi Alex, Thanks a lot for that. I will try next week.. Have a nice weekend. Philippe 2012/11/30 Bossers, Alex alex.boss...@wur.nl Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location. Changes might only be visible when restarting the instance though! Alex ** ** ** ** *Van:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *Namens *Philipe Moncuquet *Verzonden:* vrijdag 30 november 2012 5:11 *Aan:* galaxy-dev@lists.bx.psu.edu *Onderwerp:* [galaxy-dev] Changing interface design ** ** Hi ** ** I am not satisfied with some colors of the interface. I am color blind and it's hard to discriminate between job running (light yellow) and job done (light green). Well most of the time I focus on red jobs right but anyway I would like to be able to change these stuff. Can anybody point me the file I am supposed to modify to be able to do so. Many thanks in advance. ** ** Philippe ___ 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/
[galaxy-dev] Variable output number in workflows
Dear all, We've been actively developping xml wrappers for new programs in our instance of Galaxy and we encountered some problems with multiple outputs number while using these tools in a workflow. 1/ In the first case, inputs can be 1 single file or 2 paired files and the program output name is different depending on which case. The input problem is resolved using conditional and following http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files we implemented the outputs as such: outputs data name=nameSorted.single.bam format=bam from_work_dir=alignReads/alignReads.nameSorted.bam label=nameSorted single filterinputs['paired_or_single'] == 'single'/filter /data data name=nameSorted.paired.bam format=bam from_work_dir=alignReads/alignReads.nameSorted.PropMapPairsForRSEM.bam label=nameSorted paired filterinputs['paired_or_single'] == 'paired'/filter /data /outputs However, when using this tool in a workflow, the toolbox always presents the 2 outputs, whether we choose 1 or 2 inputs. Is there any way to have only one output in the toolbox but from a different file depending on the input ? 2/ the second case is very similar to the one described in http://dev.list.galaxyproject.org/outputting-different-numbers-of-files-based-on-variables-td4141375.html. When we input a single file the output is also a single file, and when we input two paired files the program outputs two files. Thanks again to the conditional tag the input problem was taken care of, but we would like the workflow toolbox to present 1 or 2 outputs (ideally with all 3 names different) depending on how many files are in the input. Is there any way to do so other than making 2 different versions of the xml or displaying all 3 outputs in the workflow toolbox ? Thanks in advance, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique - CNRS-UPMC Place Georges Teissier, 29680 Roscoff FRANCE http://abims.sb-roscoff.fr/ ___ 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/
Re: [galaxy-dev] Changing interface design
Also, those files are in fact generated from the .less files in the parent directory. Almost all colors can be customized using an ini file. The best thing to do is to create your own ..._colors.ini file and regenerate the styles into a new directory. You will need nodejs and less to do this. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Nov 30, 2012 at 6:30 AM, Bossers, Alex alex.boss...@wur.nl wrote: Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location. Changes might only be visible when restarting the instance though! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Philipe Moncuquet Verzonden: vrijdag 30 november 2012 5:11 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Changing interface design Hi I am not satisfied with some colors of the interface. I am color blind and it's hard to discriminate between job running (light yellow) and job done (light green). Well most of the time I focus on red jobs right but anyway I would like to be able to change these stuff. Can anybody point me the file I am supposed to modify to be able to do so. Many thanks in advance. Philippe ___ 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/ ___ 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/
[galaxy-dev] December 2012 Galaxy Update
Hello all, The December 2012 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12at http://wiki.galaxyproject.org/GalaxyUpdates/2012_12. *Highlights:* - 37 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Papers, including papers on Trackster and CloudMan - Two new public Galaxy Servershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Public_Galaxy_Servers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Who.27s_Hiringat seven different institutions - Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Upcoming_Events_and_Deadlines - Source Code Documentationhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Source_Code_Documentationis now available - New Galaxy Distributionhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_Distributions - New Galaxy CloudMan Releasehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_CloudMan_Release - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Other_News If you have anything you would like to see in the January *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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/
Re: [galaxy-dev] use multiple cores in BWA
That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? Thanks, Frank On Nov 30, 2012, at 3:01 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thursday, November 29, 2012, Fenglou Mao wrote: I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried Full Parameter List, anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank The number of cores isn't exposed to the end user (although in some cases it might make sense to do so), but is rather down to the Galaxy administrators (in some cases by editing the defaults in the tool XML or wrapper scripts). There was a discussion about this on the list recently. Peter ___ 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/
Re: [galaxy-dev] use multiple cores in BWA
On Fri, Nov 30, 2012 at 2:54 PM, Fenglou Mao feng...@gmail.com wrote: That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? If you modify a tool bundled with Galaxy, then when you do an hg update in simple cases it would all be handled automatically. However, if there was a change in the same part of the code, you would have to do a manual merge (the simplest route is just take the 'official' changes from the Galaxy team, and in the short term discard your local change). i.e. Not a good idea for long term maintenance. The other thread I was referring to was discussing how to move the thread settings into the Galaxy configuration files instead. Peter ___ 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/
[galaxy-dev] Issue when enabling use_tasked_jobs with torque and nfs
Hi, In my environment when I activate 'use_tasked_jobs' I'm getting this message in Info with ncbi_blast wrappers: /local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0: Job output not returned from cluster Still the dataset with the blast result is green and contains the expected information. In the log I see: galaxy.jobs.runners.drmaa WARNING 2012-11-30 13:45:32,760 Job output not returned from cluster: [Errno 2] No such file or directory: '/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout' And from torque I get this email: PBS Job Id: 1013.head Job Name: g9_toolshed_g2_bx_psu_edu_repos_devteam_ncbi_blast_plus_ncbi_blastn_wrapper_0_0_14_carlos_borroto_gmail_com Exec host: node01/0 An error has occurred processing your job, see below. Post job file processing error; job 1013.head on host node01/0 Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU Unable to copy file /var/spool/torque/spool/1013.head.ER to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmerr *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmerr': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.ER I think the problem is I'm forcing torque to use my nfs mounted shared file system: # cat /var/spool/torque/mom_priv/config $pbsserver head $usecp *:/home /home $usecp *:/local /local I can confirm this configuration is working fine with any other job not submitted through galaxy, both files are correctly copied to the working dir in that case. I'm using drmaa runner. I tried pbs, but in that case even without enabling tasked_jobs, while the err and out files are correctly copied and everything seems fine as far as I can tell, galaxy complains it can not find them. I tried increasing retry_job_output_collection, but that didn't help. Cheers, Carlos ___ 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/
[galaxy-dev] (no subject)
Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez. ___ 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/
[galaxy-dev] Containing Multiple Datasets in a Single History Item
Today we successfully set up the Barcode Splitter tool to send the outputs directly to the history, but the problem is that in some cases we want to use hundreds of bar codes, which would clutter the history. What I want to do is be able to output a text file containing the names of multiple datasets and have that sent to the history. Then, I want to create a workflow control that allows me to use that file to read multiple inputs into the workflow. So, I guess my real question is how would I create a new workflow control? Is it similar to creating a tool? Teddy___ 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/
Re: [galaxy-dev] hardware requirement for galaxy
Dear Dave, Thanks very much for your reply. It is very useful. Best, Huayan On Fri, Nov 30, 2012 at 11:14 PM, Dave Clements cleme...@galaxyproject.orgwrote: Huayan, Take a look at http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults for an idea of what infrastructure many Galaxy production servers use. That survey was taken this year. I also went to http://galaxyproject.org/search/mailinglists/ and found: http://dev.list.galaxyproject.org/Galaxy-Main-Server-Tool-Repository-td4363452.html http://user.list.galaxyproject.org/Recommended-spec-for-Galaxy-server-box-td4136963.html http://dev.list.galaxyproject.org/Local-Galaxy-concept-system-hardware-spec-questions-td4655904.html There's a lot more. Dave C On Thu, Nov 29, 2012 at 11:21 PM, Huayan Gao huayan...@gmail.com wrote: Hi there, I'm interested in the specifics of your Penn State setup. Can you send it to me? Thanks, Huayan ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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/
