- galaxy-dev - lists.galaxyproject.org

Workflow not "flowing"
by Marijn Vandevoorde 10 Aug '10

10 Aug '10

Hi all, I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why. Here's the workflow: input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course). And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data: Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values. Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either. Any ideas? Let me know if you need more info! Thanks! Marijn

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Galaxy on Mac OS
by sohkhan＠notes.cc.sunysb.edu 10 Aug '10

10 Aug '10

Hi, I am wondering if it is possible to run Galaxy on a MacPro? Sorry I am new to Mac..........been using it for last 2 days. Thanks. -Sohail

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Downloading datasets
by SHAUN WEBB 10 Aug '10

10 Aug '10

Hi, is it possible, when downloading datasets from a Galaxy library or saving datasets from a history, for the created files to be named exactly as appears in the library without the additional "GalaxyLibraryDataset..." prefix. Thanks Shaun webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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<filter> tag in output
by Davide Cittaro 09 Aug '10

09 Aug '10

Hi all, Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting: <tool id="srf2fastq" name="SRF to FASTQ"> <description>conversion</description> <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2 </command> <inputs> <param name="input1" type="data" format="srf" label="Select SRF Archive"/> <param name="filter" label="Filter out bad reads (QC fail)?" type="boolean" truevalue="Y" falsevalue="N" selected="True"/> <param name="paired" label="Is this Paired-end run?" type="boolean" truevalue="Y" falsevalue="N" selected="False"/> </inputs> <outputs> <data format="fastqillumina" name="out_file1"/> <data format="fastqillumina" name="out_file2"> <filter>paired == "Y"</filter> </data> </outputs> […] </tool> According to the wiki pages, this syntax should enable the out_file2 if the "paired" checkbox is clicked... Unfortunately I always have the tool running as the checkbox wasn't checked (i.e. out_file2 is None). If I change the filter condition to paired=="N" I always have the tool running with two outputs... Can anybody help me? thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Sort tab error?
by Minh Bui 06 Aug '10

06 Aug '10

Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format. Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png Could someone please show me how to fix this? Thank you.

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strange behavior of display_as
by Davide Cittaro 06 Aug '10

06 Aug '10

Hi there, I may need some help in debugging this: I have added some files to a library, say foo.bed. I've changed (as admin) the name from "foo.bed" to "the foo dataset". I've imported this into my current history and if I try to visualize this bed file on the genome browser, I get this error: http://host001.instruments.ifom-ieo-campus.it:8080/root/display_as?id=213&d…: 404 Not Found (host001 is the galaxy server). If I download "the foo dataset" and reupload it to galaxy, the "display_as" doesn't work (same error). Strange enough, if I import a bed file from the genome browser (say some chrom.refseq.bed) I can visualize it back (so "display_as" is working). No strange logs... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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feature request
by Davide Cittaro 06 Aug '10

06 Aug '10

Hi there, I'm manually editing some files in my data library and I've figured out a couple of feature that (IMHO) are missing: - possibility to copy/move a file from a library to another (or in a folder hierarchy) - a display of the full filesystem path of the referenced file (in the admin view, of course) d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Dynamically create Workflows
by Michael Siebauer 05 Aug '10

05 Aug '10

Hey, I wonder if it is possible to let a self-written script, dynamically create workflows. The idea is to create a pipeline, by providing the user a kind of analysis webpage where he can select a certain set of tools and parameters and the output of this interface should be a workflow. And another question. If if have a workflow consisting of a set of tools, will galaxy create a single cluster job consisting of all tools, or one job for each tool and the run them sequential? This would be important if one script pipes directly to another. Thx, Michael :-)

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GMOD Europe 2010 Registration Now Open
by Dave Clements, GMOD Help Desk 05 Aug '10

05 Aug '10

GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other expenses. Registration for all other events is free, but still required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. For an idea of what goes on at GMOD meetings, see http://gmod.org/wiki/January_2010_GMOD_Meeting. See you in Cambridge! Scott Cain and Dave Clements PS: If you have topics you want to have covered (or you want to cover) at the GMOD Meeting, or at the Satellite Meetings, please add them to the wiki pages, or contact us. We are also asking for guest speaker nominations for the meeting. -- http://gmod.org/wiki/GMOD_News <http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback

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adding another UCSC mirror to display
by Davide Cittaro 05 Aug '10

05 Aug '10

Hi again, this may be a FAQ, sorry for that... How can I add an alternate UCSC mirror site (our local mirror) to galaxy so that everything that could be displayed at UCSC-main will have the UCSC-localmirror option? Besides... how can I remove the bx main mirror? I've tried to add a ${GALAXYROOT}/tool-data/shared/campus/campus_build_sites.txt but that's not enough... I've modified the ucsc/bam.xml file adding another dynamic_link section but that's not enough... any hint? Thanks again d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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