January 2009 - galaxy-user - lists.galaxyproject.org

An idea for sharing tools
by James Casbon 10 Jun '09

10 Jun '09

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

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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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[patch] much more efficient fasta tools
by James Casbon 14 Jan '09

14 Jan '09

Hi everyone, I got bored waiting around for the fasta tools to finish so I improved the length filter and fasta to tabular scripts. On a reasonable data set these were taking over ten minutes with the old version. With this version its a few seconds. The improvement comes from not reformatting the data, caching it in memory or building a hash. All of these are unnecessary for these tasks IMO. cheers, James

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debian init scripts
by James Casbon 14 Jan '09

14 Jan '09

Hi All, Attached a debian/ubuntu init script for galaxy if your interested. You could cook up a red hat equivalent from here: http://wiki.pylonshq.com/display/pylonscookbook/Red+Hat+friendly+init.d+scr… cheers, James PS you should really bundle these with your app ;)

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