- galaxy-user - lists.galaxyproject.org

GALAXY + GBrowse
by Erick Antezana 09 Feb '09

09 Feb '09

Hi, I managed to link my local GBrowse (version 2.0) and Galaxy by following the suggestions at http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options and by adapting a bit the following files: gbrowse_build_sites.txt tool_conf.xml adding my own data source in XML... Everything seems to work fine. However, I was wondering whether there is some more documentation (screencast or whatever) to define such brigde between Galaxy and GGB? I was not sure for instance whether adding another entry to the following parameter (in universe_wsgi.ini) would also be necessary since without it, it still does the trick: gbrowse_display_sites = elegans,flybase, myDB any suggestions are very welcome! thanks, Erick

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Canales, Roger is out of the office.
by Roger D Canales 05 Feb '09

05 Feb '09

I will be out of the office starting 02/04/2009 and will not return until 02/09/2009. Please expect delays in response time.

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access_libraries.xml missing?
by Erick Antezana 05 Feb '09

05 Feb '09

Hi, I have successfully installed Galaxy, and played a bit with it (jobs, workflows, etc). However, I was curious about an error message I got when launching the daemon: IOError: [Errno 2] No such file or directory: './tools/data_source/access_libraries.xml' that file (access_libraries.xml) seems to be missing. Any suggestions? Thanks, Erick

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Fwd: [Genome] Stitch MAF blocks given a set of genomic intervals
by Stein Aerts 03 Feb '09

03 Feb '09

Dear Galaxy, I was wondering whether I might be able to get the source of the online feature "Stitch MAF blocks", to use locally? Thanks you so much, in advance! Best regards, Stein Aerts VIB, Belgium Begin forwarded message: > From: Brooke Rhead <rhead(a)soe.ucsc.edu> > Date: Sat 31 Jan 2009 01:09:25 GMT+01:00 > To: Stein Aerts <stein.aerts(a)med.kuleuven.be> > Cc: genome(a)soe.ucsc.edu > Subject: Re: [Genome] Stitch MAF blocks given a set of genomic > intervals > > Hello Stein, > > There is not a tool to do this in the Kent source tree. From one of > our developers: > > --- > We don't have good tools to do this, partially because the > transformation isn't necessarily possible (not all maf's can be > converted to a global alignment like FASTA is, and also maf blocks > don't necessarily contain all the sequence that are in the species). > > The user may grab the corresponding sequences using the maf, and run > their own global aligner (e.g. clustalw, MUSCLE). > --- > > You might be able to get Galaxy's source for this. If you haven't > already contacted them, their helpdesk address is galaxy-user(a)bx.psu.edu > . > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/30/09 03:25, Stein Aerts wrote: >> Hi, >> I am looking for a standalone solution to extract MAF blocks and >> then 'stitch' those together for each species into a fasta file, >> starting from a genomic interval of one species? Galaxy has this >> feature online so I was wondering whether there is a script or >> similar code in the Kent source (or a combination of scripts) to >> accomplish this locally in an efficient way? >> Many thanks in advance, >> Stein Aerts >> Belgium >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> _______________________________________________ >> Genome maillist - Genome(a)soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome > Stein Aerts, PhD Laboratory of Neurogenetics VIB-KULeuven Belgium http://perswww.kuleuven.be/~u0038182/ http://med.kuleuven.be/cme-mg/lng/

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display at UCSC main (gbrowse)
by Rochak Neupane 30 Jan '09

30 Jan '09

When a data is in BED format or Customtrack and build is on of ucsc, a link shows up with a link to "display at UCSC main". I was wondering if this would be possible to do with gbrowse for data in Gff or Gff3. I added gbrowse links to: tool-data/shared/gbrowse/gbrowse_build_sites.txt for data in gff format, lib/galaxy/datatypes/interval.py has add_display_app in it, but I was not able to get a link on my dataset. What exactly do I have to do to get a link to "display in Gbrowse"? thanks! rochak

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strange behavior with Job-queue
by Assaf Gordon 27 Jan '09

27 Jan '09

Hello, On a local galaxy server, I've got into a strange situation: Several jobs are marked as "new", but non are starting. I've stop and re-started the server, and got the following message: ----- galaxy.jobs.runners.local DEBUG 2009-01-26 19:29:00,829 5 workers ready galaxy.jobs.schedulingpolicy.roundrobin INFO 2009-01-26 19:29:00,829 RoundRobin policy: initialized galaxy.jobs INFO 2009-01-26 19:29:00,829 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs INFO 2009-01-26 19:29:00,829 job manager started galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7886 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7893 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7896 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7902 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7904 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7905 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7906 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7907 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7908 is still in new state, adding to the jobs queue galaxy.jobs INFO 2009-01-26 19:29:00,971 job stopper started ----- But even after a server restart - no jobs are starting (I've waited for about a minute after restart). Is there any configuration setting that can cause these jobs to start if I restart the server? (or cause the 'stale' jobs to be deleted?) Thanks, Gordon.

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Two usability questions
by Assaf Gordon 27 Jan '09

27 Jan '09

On my local galaxy server: 1. Is there a way to limit number of concurrent jobs PER user ? That is - if one user started a workflow with 30 steps, Executing only one (or two or three) jobs of that user, instead of all his jobs hogging the job-queue (and causing other users' jobs to wait). 2. Is there a way to force users to login? Prevent un-logged in users from running jobs ? Thanks, Gordon.

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file format on biomart imported data
by Rochak Neupane 22 Jan '09

22 Jan '09

Hello, When importing BioMart data from galaxy, the format is always "text". In the "Results" page in BioMart where it says "Export al results to Galaxy, the only available format is "TSV". Export all results to Galaxy HTMLCSVTSVXLS Unique results only Should this not make the data imported to galaxy to be "tabular"? With the default "text" format, I cannot view the data within galaxy, I have to download it first then open in an editor. Only when the I change the data type to "tabular" do I get to view the data within galaxy. I downloaded same data as both "text" formatted and "tabular" formatted and there are no differences between the files. It would be better if galaxy could automatically change the datatype to "tabular" when getting data from biomart. When sequences are imported, perhaps galaxy can detect it as such and apply the "fasta" format. Biomart always exports sequences in fasta format but in galaxy this also comes out as text. Thanks. Rochak

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Help with adding new datatype
by Chris Cole 20 Jan '09

20 Jan '09

Hi, I'm confused on how to add a new datatype. I've read the http://g2.trac.bx.psu.edu/wiki/AddingDatatypes wiki page, but it isn't clear what I need to do for a completely new type. Specifically, I want to add a gzip tool to compress and uncompress files to help up/downloading of large files. I've added the following line to the datatypes_conf.xml: <datatype extension="gz" type="galaxy.datatypes.images:Gzip" mimetype="application/gzip" display_in_upload="true"/> But I am stumped as to where I should add the additional information as per step 3. on the wiki page. Can someone help, please? BTW I do code, but not in python. Thanks, Chris

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Lost sequence info on update
by Chris Cole 16 Jan '09

16 Jan '09

Hi, I've recently done an svn update on my local Galaxy install, which all seemed to go well. However, in the history pane, the information for fasta and solexafastq files no longer details the number of sequences in the file, it only gives the size of the file. How do I get back the sequence information for those file types? Thanks, Chris

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