January 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] GalaxyToolShed: 'Contact owner'
by Greg Von Kuster 13 Jan '12

13 Jan '12

Hi Marcel, Requiring users to be logged in in order to contact the owner of a repository significantly hinders spam emails. On Jan 12, 2012, at 9:04 PM, Marcel Schumann wrote: > Hi Greg, > > sure, that's right. > But I checked it for my own repository _without_ being logged in ... and for other repositories the option was also not available. > > Ah, ok, now I see where the problem is: it seems that you have to be logged in in order to contact the owner of a repository! Ok, is this really intended? ;-) > > If yes, then the problem is of course that most users who want to search for new galaxy tools will not be logged in (because they probably have no account) and thus cannot contact the owner ... and will not even know that there exists such an option. > > > Cheers, > Marcel > > On 1/12/12 5:55 PM, Greg Von Kuster wrote: >> Hello Marcel, >> >> This option is available for all repositories. If you are looking at a repository you own, the option is not available because it makes no sense to contact yourself. However, anyone else looking at your repository has the option available to them. >> >> Thanks! >> >> Greg >> >> On Jan 12, 2012, at 11:21 AM, Marcel Schumann wrote: >> >>> Dear Greg, >>> >>> I just noticed that for some repositories there is a 'contact owner' option, which is a very nice idea, I think ... >>> >>> However, for my repositories (CADDSuite) this option is not available. Is there any way I can enable this ? >>> >>> >>> Cheers, >>> Marcel >>> >>> >>> >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > > > -- > Marcel Schumann > > University of Tuebingen > Wilhelm Schickard Institute for Computer Science > Division for Applied Bioinformatics > Room C313, Sand 14, D-72076 Tuebingen > > phone: +49 (0)7071-29 70437 > fax: +49 (0)7071-29 5152 > email: schumann(a)informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Re: [galaxy-dev] Picard MarkDups
by Ann Black 12 Jan '12

12 Jan '12

Hi Ryan - I have done similar things with our tools as well. For now I have edited the xml file to include the following option in the <command> section that would get passed into the picard script wrapper: --maxjheap="8g" I considered exposing this out in the UI, but have teetered on whether to expose the complexity out to the end user. Thanks, Ann > >Message: 8 >Date: Thu, 12 Jan 2012 11:37:23 -0500 >From: Ryan Golhar <ngsbioinformatics(a)gmail.com> >To: galaxy-dev(a)lists.bx.psu.edu >Subject: [galaxy-dev] Picard MarkDups >Message-ID: > <CAFbjochhOioiw7a8t4p0gVs8ZAYWUx82gv4Bjv1RnUZjxC0G-Q(a)mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >I'm trying to run Picard MarkDups through Galaxy. Picard is using the >standard 4g for the java max heap size. I need to increase this. Is it >possible to offer this as an option to the user? If not, where do I >change >this? I see the entry in picard_wrapper.py. Do I change it here or in >the >XML file for MarkDups? > >Ryan >

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Toolshed tools are not run
by Anthonius deBoer 11 Jan '12

11 Jan '12

Hi, I am trying to install some tools from the main toolshed, and the installation went OK for the tool "tabToHtml (really something that galaxy should do out of the box...Show tab data in actual tables, rather than a dump of text). But when I try to run the tool, it is just marked as queued only and never actually runs...Anyone know what this could be? Using the latest galaxy-central on a local installation with an SGE cluster. Thon

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AnnoVar tool?
by Ryan Golhar 11 Jan '12

11 Jan '12

I thought I once saw a publication (or presentation maybe) talking about AnnoVar being available in Galaxy but I don't see it online or in galaxy-dist, nor in the tool shed. Is it really available?

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How to set output name programmatically in workflows using the API?
by Carlos Borroto 11 Jan '12

11 Jan '12

Hi, I would like to use the "Rename Dataset" action with a value base on the input. I was wondering if there is a way to do this programmatically? Searching the list I found this enhancement request that I think could help me, any update on this feature? https://bitbucket.org/galaxy/galaxy-central/issue/623/expose-more-fields-to… Thanks, Carlos

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Job in Edinburgh, Scotland
by Alastair Kerr 11 Jan '12

11 Jan '12

Dave Clements kindly suggested that I post this to the list. My team is looking for someone to help out with the ever increasing need of data analysis in our centre. We support the diverse bioinformatics needs of 18 groups (http://www.wcb.ed.ac.uk) and currently there are many large NGS projects. We use galaxy as a central component for rapid tool development and to enable users in their own research. Dave (clements(a)galaxyproject.org) has also kindly offered to provide impartial advice about Edinburgh for those who may not know of the joys of living here. It is a fixed term contract for 30 months (which should allow plenty time to impress groups leaders for more funding). -Alastair -- Alastair Kerr, Ph.D., Bioinformatics Core Facility Manager, Wellcome Trust Centre for Cell Biology, 2.21 Michael Swann Building, The University of Edinburgh, Edinburgh, EH9 3JR, UK Tel: +44 131-650-7527 Details: =-=-=-=-=-=-=-=-= Wellcome Trust Centre for Cell Biology, University of Edinburgh: Bioinformatics Support Provider A position is available in bioinformatics support for the Wellcome Centre for Cell Biology at the University of Edinburgh. The successful candidate will work for the Bioinformatics Core Facility to help provide advice, training, analysis and applications to Centre laboratories (see www.wcb.ed.ac.uk ) A key area for support in the centre is the increase in projects using a range of next-generation sequencing techniques (ChIP-seq, RNA-seq etc) and hence skills pertaining to managing and analysing such data is highly desirable. Funding for this post is, in part, from the EpiGeneSys Network of Excellence (www.epigenesys.eu ) to the Allshire Lab (http://allshire.biology.ed.ac.uk ). Thus the successful applicant will have access to a variety of training courses, scientific workshops and forums run by EpiGeneSys. Qualifications: Candidates should have at least an M.Sc. in computational biology/bioinformatics or equivalent. An understanding of molecular biological processes would also be useful but not essential. Essential skills: Some background in molecular biology and statistics. Experience in the Linux command line and at least one scripting language (Perl, Python or Ruby). Desirable skills: R-language including BioConductor, databases (mySQL or postgres), Galaxy platform administration, Linux administration Salary Scale: Estimated salary: £30,000 to £34,000 GBP - To be confirmed. Fixed Term: 30 months. Please contact Robin Allshire robin.allshire(a)ed.ac.uk or Alastair Kerr alastair.kerr(a)ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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User name / public name confusion.
by J. F. J. Laros 11 Jan '12

11 Jan '12

Dear developers, Subject: Minor issue - Confusion about public / user name. Description: When creating an account or managing user information, the error ``User name must contain only lower-case letters, numbers and '-''' may occur if the user chooses an invalid public name. This error can be confusing when the user tries to search for a ``User name'' field. Perhaps this error should mention the field name. With kind regards, Jeroen. -- Jeroen F. J. Laros - J.F.J.Laros(a)lumc.nl

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SAM/BAM Hybrid Selection Metrics
by Ryan Golhar 10 Jan '12

10 Jan '12

Hi all - I think there is a problem with the Picard HSMetrics wrapper in Galaxy. The wrapper accepts a BAM files and a BED file. However the BED file isn't really in a BED format...it requires a SAM header before the BED lines. This really isn't a BED file format. I'm not quite sure how Galaxy should deal with this...maybe a file format specific for Picard formatted BED file.

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Status on importing BAM file into Library does not update
by Ryan Golhar 10 Jan '12

10 Jan '12

I'm adding Data Libraries to my local galaxy instance. I'm doing this by importing directories that contain bam and bai files. I see the bam/bai files get added on the admin page and the Message is "This job is running". qstat shows the job run and complete. I checked my runner0.log and it registers the PBS job completed successfully. But the web page never updates. I tried to refresh the page by navigating away from it then back to it, but it still reads "This job is running". How do I fix this?

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Setup galaxy to run on SGE cluster
by Derrick LIN 10 Jan '12

10 Jan '12

Hi guys, I am trying to configure our test galaxy to run on our SGE cluster http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. This is my first time to come across to drmaa, so a bit confused. I installed teh galaxy on a NFS location where can be accessed clsuter-wide. I have configured in universe_wsgi.ini: start_job_runners = drmaa default_cluster_job_runner = drmaa:/// and export the libdrmaa path: export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx-amd64/libdrmaa.so.1.0 Sound like that's all. But I am not sure how galaxy can actually bind to my cluster? Anywhere I need to specify the qmaster URL etc? Or simply configure galaxy host to be a submission host of the cluster, the galaxy will fetch all information by itself? Kind regards, Derrick

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