November 2011 - galaxy-user - lists.galaxyproject.org

Trouble in extracting species on maf imported from UCSC
by 4urelie K 14 Nov '11

14 Nov '11

Hi, When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to "Filter MAF blocks by Species" the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve? Thank you, Aurelie

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Asynchronous data source
by Joachim Baran 14 Nov '11

14 Nov '11

Hello! I am adding support for Galaxy's asynchronous data sources to a server of mine, but I cannot get Galaxy to retrieve the actual data from it. So far, I have added a data source tool to my Galaxy installation which links out to my server. There I track the URL that is provided by Galaxy and later I use this URL to tell Galaxy that the data can be retrieved. At this point, Galaxy returns an HTML document to me, which says (excerpt): "[...] <p>The following job has been successfully added to the queue:</p> <div style="padding: 10px"><b> 1: testserver</b></div> <p> You can check the status of queued jobs and view the resulting data by refreshing the <b>History</b> pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered. </p> [...]" I just discard this HTML. When I then go back to my Galaxy server, nothing has happened. Even when I refresh, I do not see any job pending. Does anyone know why Galaxy would not retrieve the data? Do I really have to show the HTML that is returned by Galaxy to make it work? Thanks, Joachim

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Re: [galaxy-user] Lastz
by Nate Coraor 14 Nov '11

14 Nov '11

On Nov 11, 2011, at 10:01 AM, Andrew South wrote: > Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones will likely queue until free slots are available. Please let us know if there's further trouble, and thanks for using Galaxy, --nate > > ************************************************************ > Please consider the environment. Do you really need to print this email? > > > >>> Nate Coraor <nate(a)bx.psu.edu> 11/11/2011 14:55 >>> > On Nov 11, 2011, at 9:21 AM, Andrew South wrote: > > > Hello folks > > > > Anyone else having trouble with running Lastz to map? > > > > Jobs are being sent but not running. > > > > It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. > > Hi Andy, > > It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. > > --nate > > > > > Thanks, > > > > Andy > > > > > > Dr A P South > > Centre for Oncology and Molecular Medicine > > University of Dundee > > Ninewells Hospital & Medical School > > Dundee > > DD1 9SY > > Tel 01382 496432 > > Fax 01382 633952 > > > > a.p.south(a)dundee.ac.uk > > > > > > ************************************************************ > > Please consider the environment. Do you really need to print this email? > > > > The University of Dundee is a registered Scottish charity, No: SC015096 > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > The University of Dundee is a registered Scottish charity, No: SC015096 >

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generic filenames with Export to File
by Danielle Lemay 14 Nov '11

14 Nov '11

Hello, When using Export to File, it appears that galaxy renames each output file to something generic datXXX.dat and changes the filename extension (to .dat). How do I convince Galaxy to preserve my filenames so I know which file is which ? Is there some other way to download multiple output files and preserve their names and file extensions? Thanks, Danielle ######################################################### Danielle G. Lemay, PhD Assistant Professional Research Scientist, UC Davis Genome Center University of California at Davis (530) 220 3438 dglemay(a)ucdavis.edu

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(no subject)
by gaurav thareja 13 Nov '11

13 Nov '11

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Cufflinks Annotation problem
by Bidwell, Christopher A. 12 Nov '11

12 Nov '11

Colleagues, I am having trouble running cufflinks with an annotation file on the public Galaxy. The assembled transcripts gtf file has all the FPKM at 0 although the gene expression and transcript expression tab files have values for FPKM. I have seen the SEQanswers threads about the compatibility of tophat bam files relative to chromosomes labeled as 1,2,3… versus Chr1, Chr2, Chr3… I am using the iGenomes bovine UMD3.1 genome and annotation file (chromosomes are 1,2,3) from the history. I altered the gtf file to Chr1, Chr2, Chr3… but it did not help. Another potential discrepency/conflict is that the genome and gtf file have the bosTau6 database attribute from when I uploaded them. However I am running them from the history (bosTau6 is not an option for tophat). I do not seem to be able to remove the attribute. Am I missing something else? Here is the command line Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 8 -G /galaxy/main_database/files/003/142/dataset_3142240.dat -N -b ref.fa Here is the details page Tool: Cufflinks Name: Cufflinks on data 69, data 4, and data 5: assembled transcripts Created: Nov 09, 2011 Filesize: 44.6 Mb Dbkey: bosTau6 Format: gtf Tool Version: Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 4: Tophat for Illumina on data 4 and data 69: accepted_hits Max Intron Length 50000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Annotation 5: iGen_UMD3_1_genes.gtf Conditional (bias_correction) 0 Conditional (seq_source) 1 Using reference file 69: UMD31_iGen_1-29X.fa Conditional (singlePaired) 0 Cordially, Chris

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Adding new data source
by Joachim Baran 11 Nov '11

11 Nov '11

Hello! I have extended a service to support asynchronous data depositing (http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources) but I cannot quite figure out how to access it from the Galaxy web-site. Can someone point me to the right documentation for integrating the service into Galaxy, please? I seem to be out of luck with googling today.. Thanks, Joachim

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MA2C peak calling or nimbelgen chip on chip analysis
by shamsher jagat 11 Nov '11

11 Nov '11

Do we have option of running MA2C peaks in Galaxy or is tehre an option of analyzing Chip on Chip data from Nimbelgen. Thanks

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BWA question on Mac OS X 10.7.2
by Christopher Callaway 11 Nov '11

11 Nov '11

Hi, I have tried to install BWA on my MacPro. Once installed, I typed the command make and it did not work. When installing BWA to a Linux machine, it worked fine. How do I get around this problem? Thanks, CWC

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Lastz
by Andrew South 11 Nov '11

11 Nov '11

Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Thanks, Andy Dr A P South Centre for Oncology and Molecular Medicine University of Dundee Ninewells Hospital & Medical School Dundee DD1 9SY Tel 01382 496432 Fax 01382 633952 a.p.south(a)dundee.ac.uk ************************************************************ Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096

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