August 2010 - galaxy-user - lists.galaxyproject.org

question about lastz parameters
by Heather Kent 06 Aug '10

06 Aug '10

Hi, I've been using lastz to map some 454 reads to a reference sequence on galaxy. I'm not clear on what the mapping modes do for the analysis. If I am already setting a cut-off value for the percent identity for reporting matches then what exactly does the mode setting do? In the tutorial you set a roche-454 98% mode based for a re-sequencing example and then set the identity to 90%, what parameters in lastz does the mapping mode change? thanks, H -- Heather Kent Bioinformatics Core Facility Public Health Agency of Canada National Microbiology Laboratories (204)784-7503 Quote of the week: Most people are other people. Their thoughts are someone else's opinions, their lives a mimicry, their passions a quotation. Oscar Wilde (1854 - 1900), De Profundis, 1905

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Re: [galaxy-user] No such test TestForTool_snpFreq
by Kelly Vincent 05 Aug '10

05 Aug '10

Belinda, You will see this message when there is some error in the XML file. If you can make it valid XML, the test framework will be able to find the test. Regards, Kelly On Aug 5, 2010, at 3:43 PM, galaxy-user-bounces(a)lists.bx.psu.edu wrote: > The attached message has been automatically discarded. > From: "Belinda M. Giardine" <giardine(a)bx.psu.edu> > Date: August 5, 2010 3:43:20 PM EDT > To: Galaxy-user(a)bx.psu.edu > Subject: No such test TestForTool_snpFreq > > > The tool snpFreq is there, the test is set up in snpFreq.xml. The > tool is listed in tool_conf.xml.sample. But I still get this > error. I can test other tools with no problem. Any ideas? > The command I am using: > sh run_functional_tests.sh -id snpFreq > > Belinda > > >

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Data management
by E.Kok＠antrg.umcn.nl 05 Aug '10

05 Aug '10

Hello Galaxy, I must say, I am quite enthousiastic about your software. Looking at the possibilities I am at this moment quite positive we can use the program. I do have one question though, and that involves data management. I can't seem to find information about data privacy within Galaxy. As you might understand, the data generated here is used for publications and we wouldn't want results to leak before an article is published about it. So I am wondering how secure the data on your servers is. I hope to hear from you soon. Best regards, Esther Kok Radboud University Nijmegen, the Netherlands Department of Human Genetics Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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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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Conditional variables not available on the command line?
by Jacob Biesinger 03 Aug '10

03 Aug '10

Hi! I have a tool with three possible types of input. A flag is set to either 'bed', 'resource' or 'file' for the two inputs. I've noticed that the conditional variables are not available on the command line, so is there some other way of setting these flags? So far, the UI handles the 3 possible input types nicely, but I'd like to set the format1 and format2 flags directly from the conditional. It seems that the conditional parameters aren't seen by cheetah. I also tried using 'hidden' parameters, but those seem to be for totally different uses. # USAGE: # python enrichment_pairwise.py myfile.bed geneExons --format1=bed --format2=resource --genome_resource=hg18 --output_file=overlap.txt Trying to run this in galaxy gives: Traceback (most recent call last): File "/home/wbiesing/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/home/wbiesing/galaxy_dist/lib/galaxy/jobs/__init__.py", line 355, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/wbiesing/galaxy_dist/lib/galaxy/tools/__init__.py", line 1397, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/wbiesing/galaxy_dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/wbiesing/galaxy_dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1280646041_98_13115.py", line 89, in respond NotFound: cannot find 'res1_select My tool's XML file looks like: <command interpreter="python">enrichment_pairwise.py $resource1 $resource2 --format1=$res1_select --format2=$res2_select --genome_resource=$dbkey --output_file=$outputFile</command> <inputs> <conditional name="resource1_test"> <param name="res1_select" type="select" label="Input type for resource1"> <option value="bed">BED File</option> <option value="resource">Worldbase Resource</option> <option value="file">File with list of Worldbase Resources</option> </param> <when value="bed"> <param name="resource1" type="data" format="bed" label="Bed file for resource1" /> </when> <when value="resource"> <param name="resource1" type="text" label="Worldbase ID for resource1" /> </when> <when value="file"> <param name="resource1" type="data" format="text" label="Text file with Worldbase IDs to iterate over for resource1" /> </when> </conditional> <conditional name="resource2_test"> <param name="res2_select" type="select" label="Input type for resource2"> <option value="bed">BED File</option> <option value="resource">Worldbase Resource</option> <option value="file">File with list of Worldbase Resources</option> </param> <when value="bed"> <param name="resource2" type="data" format="bed" label="Bed file for resource2" /> </when> <when value="resource"> <param name="resource2" type="text" label="Worldbase ID for resource2" /> </when> <when value="file"> <param name="resource2" type="data" format="text" label="Text file with Worldbase IDs to iterate over for resource2" /> </when> </conditional> </inputs> Thanks for your help! -- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587

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Help needed
by Rehman, Atteeq (NIH/NIDCD) [F] 02 Aug '10

02 Aug '10

Hello, I have a list of variants(SNPs) that differ from reference sequence (in my human subject DNA) and I want to filter out the known variants reported in dbSNP, so that I can have a short list of putative novel variants. Could somebody please tell me how can I do this? [cid:image001.jpg@01CB30BC.5FD96A20] Atteeq Ur Rehman Visiting Fellow National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Room 2A-19, 5 Research court, Rockville, MD, USA, 20850. Lab Ph. No. 301-402-9059

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processing GFF3 file of variants
by Paul Webster 02 Aug '10

02 Aug '10

Hello all, I have a GFF3 file of variants from nextgen sequencing and want to find non-synonymous changes. Any suggestions? One possible way would be: 1. Use tool "Compute an expression on every row" to extract the reference allele and sample allele from column 9 (attributes column) of the GFF3 file 2. Download some codons (see help for "mutate codons" tool for more info about this) 3. Use the "mutate codons" tool to mutate the codons with the variants extracted from the GFF file. Here is the problem:- The help examples for the tool "compute an expression on every row" are very simplistic. This tool is much more powerful. Where can we find information about how to extract substrings with this tool?

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