July 2011 - galaxy-dev - lists.galaxyproject.org

Multiple fastq files per forward/reverse mates (tophat and related tools)
by W. Augustine Dunn III 15 Jul '11

15 Jul '11

I want to customize the tophat and related interfaces to allow more than one fastq file per fwd/rev set as is allowed and very helpful in the CLI version: $ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq Is there a way to select multiple items from a dropdown menu or can/should i convert that part of the interface to a text input field so I can simply feed the command a list of files like on the command line? This last method seems like it might be a little unsafe though. But even if its not, it divorces the file management from the history which seems like its not a good idea. Has anyone done this? Thanks, Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*

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fyi: can't upload to toolshed
by Edward Kirton 15 Jul '11

15 Jul '11

Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here)

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Sending Data to Galaxy
by Amirhossein Kiani 14 Jul '11

14 Jul '11

Hey Galaxy developers! I was wondering if anyone knows how to send data to a local galaxy instance from another server (I'm interested in sending a BAM file to Galaxy). I see that UCSC and others have done it but couldn't find anything about the API doc they are using... Looking at the request headers from UCSC, I see that this request: tool_id:bx_browser URL:http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables hguid:883956 db:hg18 org:Human hgta_table:seq hgta_track:gold hgta_regionType:genome hgta_outputType:primaryTable position:chr10:90997300-90997350 hgta_doTopSubmit:get output hgsid:62857 hgta_doGalaxyQuery:Send query to Galaxy has been sent to: http://main.g2.bx.psu.edu/tool_runner Is this all needed? If so how is the URL to the data file passed to Galaxy? Many thanks! Amir

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more cleanup scripts messages
by Assaf Gordon 14 Jul '11

14 Jul '11

Hi Greg (again), This patch adds messages for the "purge histories" step: 1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong). 2. in "info_only" mode, a message is printed about each deleted history 3. in "info_only" mode, a message is printed for each HDA that is checked 4. The message for HDA is changed to include the associated dataset id. Comments are welcomed, -gordon

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Saved Histories - default view on deleted histories (bug)
by Michal Stuglik 14 Jul '11

14 Jul '11

hi all, in galaxy-central: 1. default view in "Saved Histories" section is set on deleted items ( Jeremy, I did double check this morning on fresh instance :)) 2. in advanced search option: one of the filter switch is deleted and does the same job as active switch 3. Sugestion: Saved Histories->Advanced Search sharing: private | shared | accessible | published | all deleted: active | deleted | all maybe it is better to change it to: sharing: private | shared | accessible | published | all status: active | deleted | all I think "deleted" is not clear.. all the best, michal

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toolExample.pl script bug report
by Casey Bergman 14 Jul '11

14 Jul '11

Dear Galaxy Team - We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences. If you could confirm this and modify if possible, this might help other users. All the best, Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman Email: casey.bergman(a)manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/

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Possible to re-use toolconfig xml files outside Galaxy?
by Samuel Lampa 14 Jul '11

14 Jul '11

Hi, I have been looking into re-using the galaxy toolconfig xml files outside galaxy, for auto-generating wizards for command line tools, in an own little (eclipse based) software (For a short background, see [1]). I have come to realize though that the xml-files are not really independent, but (almost?) always is accompanied by a correpsonding .py file, which does more or less tricks, which seemingly makes it very hard to use the xml-files outside a galaxy/python environment at all. My questions: 1. Are the xml-files *always* accompanied by the .py file, or is that optional? 2. Would my idea be possible/reasonable at all? 3. Are there other more general tool config formats that I could use, since I'm not using galaxy atm? 4. Any other suggestions or ideas? Best Regards // Samuel [1]: The tool is built as a complement to some galaxy initiatives at the UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to configure batch scripts for the software installed at UPPMAX, of which bioinformatics tools are just a part. The galaxy toolconfig xml-format looked useful though, and seemed to enable us to have at least most of our bioinformatics tools (the category with most installed tools at UPPMAX) already configured. -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa(a)scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se

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removing "Select All" / "Unselect All" buttons from a set of check boxes
by Hans-Rudolf Hotz 13 Jul '11

13 Jul '11

Hi Is there a way to remove the "Select All" and "Unselect All" buttons from a set of check boxes? - crated with: <param name="samples" type="select" display="checkboxes" multiple="true" dynamic_options="ds_samplesFromServer()"/> I have a very long list, and I don't want to encourage people to tick all boxes. Thank you very much for your help, Hans

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empty status for non-empty datasets
by Shantanu Pavgi 13 Jul '11

13 Jul '11

Hi, In our local galaxy install (currently revision 50e249442c5a) we are seeing few output datasets as 'empty' in the galaxy web interface. The actual file size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by clicking on download/view icons, however they can't be imported in other workflows. I looked into the database and figured out that file_size column value for corresponding dataset id is zero. I am guessing that's why it is being shown as empty in the web interface. Any suggestions on how to resolve this will be helpful. -- Thanks, Shantanu.

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Re: [galaxy-dev] LAJ Error
by Ellul Jason 13 Jul '11

13 Jul '11

Hi All, I have been able to workaround the problem I was having by modifying the LAJ_code.py to include 'and data != None' on each of the elif statements. i.e. if name == "maf_input": params["alignfile1"] = "display?id=%s" % data.id elif name == "seq_file1" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq1"] = "display?id=%s" % data.id elif name == "seq_file2" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq2"] = "display?id=%s" % data.id elif name == "exonfile" and data != None and data.state == data.states.OK and data.has_data(): params["exonfile"] = "display?id=%s" % data.id elif name == "repeatfile" and data != None and data.state == data.states.OK and data.has_data(): params["repeatfile"] = "display?id=%s" % data.id elif name == "annotationfile" and data != None and data.state == data.states.OK and data.has_data(): params["annotationfile"] = "display?id=%s" % data.id elif name == "underlayfile" and data != None and data.state == data.states.OK and data.has_data(): params["underlayfile"] = "display?id=%s" % data.id elif name == "highlightfile" and data != None and data.state == data.states.OK and data.has_data(): params["highlightfile"] = "display?id=%s" % data.id For some reason, even though repeatfile is optional the script always thinks that a file has been selected, even when one has not. Hence data is equal to None and it throws a 'nonetype has no attribute state' error when it checks data.state==data.states.OK. Could a developer please look into why it would think a file for the option repeatfile had been selected when one hasn't. Cheers, -- Jason Ellul Bioinformatician Cancer Research Division Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul(a)petermac.org Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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