- galaxy-user - lists.galaxyproject.org

sicer dose not support chicken genome
by Chen, Jingchen 20 Feb '13

20 Feb '13

Hi all I just found that I could not use sicer to call peaks from chicken data. It says 'sicer dose not support the genome'. Could anyone fix this? Best Jingchen

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mitochondrial transcripts
by Brown, Tim 19 Feb '13

19 Feb '13

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error in .vcf .bcf files from freeBayes and mPileup
by stefano cardinale 19 Feb '13

19 Feb '13

Hi, I run a very regular BWA mapping with a public reference genome sequence and then I tried to do some variant analysis with both mpileup and freeBayes tools. These jobs run just fine, but then when I went to convert these files to a .maf format or using the bcf2vcf converter there were errors in the metadata and the jobs couldn't run. One main error in the freeBayes output gave the exception: "components must have same text length". I also tried to run some vcf to maf converter from command line (python tool) on the downloaded file and also didn't work. Any suggestion on what's wrong with the file? thanks stefano

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Uploading large archive histories
by Innocent Onsongo 19 Feb '13

19 Feb '13

Galaxy Team, I exported a large history that reduced to an 8GB compressed file. I would like to re-import this history but the "Import from file" options gives me an error (see attached image). I looked around the wiki and there appears to be an ftp upload for large files (http://wiki.galaxyproject.org/FTPUpload) Is there an equivalent FTP upload for exported large histories? I would like to export some of my large analysis histories and save them in an external hard drives to free some space in my account. However, I am not able to re-import large histories. I want to make sure I can re-import these large histories before I delete them from my Galaxy account. Getiria -- Getiria Onsongo, Ph.D. Informatics Analyst, Research Informatics Support System Minnesota Supercomputing Institute for Advanced Computational Research University of Minnesota Minneapolis, MN 55455 Phone: 612-624-0532

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replicates in cuffdiff output
by Johanna Sandgren 18 Feb '13

18 Feb '13

Hi, I am running cufflinks and cuffdiff using Galaxy. I am however wondering if it is not supposed to be output files from cuffdiff regarding each replicate. Anyone know why those (read.group-files) are not there, or when they will be if it is because of the version used in Galaxy. I find it very valuable to have those to be able to see intra/inter-group features in downstream analysis. Thanks, Johanna ...................................................................................................................................................... Johanna Sandgren, PhD Department of Oncology-Pathology CCK, Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office), +46-8- 321047(fax), +46-708 388476 (mobile)

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extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan 15 Feb '13

15 Feb '13

I have successfully uploaded a large fasta file (2.5 million genomic sequence contigs) onto Galaxy server. I wish to extract a subset of sequences from this file. I have a list of the fasta headers. Is there a way I can accomplish this on Galaxy? -- Perumal Vijayan Saskatoon Canada

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Rscript not found when running shell script in Galaxy
by Makis Ladoukakis 14 Feb '13

14 Feb '13

Dear users, Has anyone encountered this problem before? I wrote a shell script which among other things calls some R scripts like this.. Rscript rscript_to_use.R When I run it via terminal it's fine plus I have verified Rscript works. But when I upload my tool to Galaxy and try to run it I get the following error: /path/to/script/shell_script.sh: line 26: Rscript: command not found Can anyone help? Thank you in advance, Makis Ladoukakis

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galaxy-user submission
by Oya Uyguner 14 Feb '13

14 Feb '13

I would like to enroll, galaxy-user mailing list. Regards, Z. Oya Uyguner Department of Medical Genetics Istanbul Medical Faculty Istanbul University Bu elektronik posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafindan alinmasi amaçlanan yetkili gerçek ya da tüzel kisinin kullanimi içindir.Eger söz konusu yetkili alici degilseniz bu elektronik postanin içerigini açiklamaniz, kopyalamaniz, yönlendirmeniz ve kullanmaniz kesinlikle yasaktir ve bu elektronik postayi derhal silmeniz gerekmektedir. ISTANBUL ÜNIVERSITESI bu mesajin içerdigi bilgilerin dogrulugu veya eksiksiz oldugu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne sekilde olursa olsun içeriginden, iletilmesinden, alinmasindan ve saklanmasindan sorumlu degildir. Bu mesajdaki görüsler yalnizca gönderen kisiye aittir ve ISTANBUL ÜNIVERSITESI'nin görüslerini yansitmayabilir. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------! ----------------------- This message and attachments are confidential and intended solely for the individual(s) stated in this message.This email is not intended to impose nor shall it be construed as imposing any legally binding obligation upon ISTANBUL UNIVERSITY and/or any of its subsidiaries or associated companies. Neither ISTANBUL UNIVERSITY nor any of its subsidiaries or associated companies gives any representation or warranty as to the accuracy or completeness of the contents of this email. ISTANBUL UNIVERSITY will not be held liable to any person resulting from the use of any information contained in this email and will not be liable to any person who acts or omits to do anything in reliance upon it.

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Problem
by Christopher O'Toole 13 Feb '13

13 Feb '13

Hi, Can you help me? I'm using the main Galaxy server for RNA-Seq analysis and I'm having trouble. I'm running top hat analysis, followed by cuff links, cuff compare and finally cuffdiff. I'm unable to retrieve gene names from the final cuffdiff analysis. I have tried using genome annotation with cuff links and cuff compare, but I either run into a duplicate error or the result does not include gene names. I am new to this, I have only been using Galaxy for a week, so could any suggestions be simplistic please! Thanks! Christopher O'Toole.

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Fwd: Installing new tools from the tool shed
by David Joly 13 Feb '13

13 Feb '13

Thanks Dannon! One step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer)... But now it says: ValueError: too many values to unpack 2013/2/13 Dannon Baker <dannon.baker(a)gmail.com> > On Feb 13, 2013, at 6:16 PM, David Joly <idjoly(a)gmail.com> wrote: > > > Hi! > > > > Ok, I know many people had the same issue, but I just can't figure > what's going on. I'm quite new about using a local instance of Galaxy and > I'm trying to figure how to install a tool from the tool shed. Reading the > tutorial (Installing Galaxy tool shed repository tools into a local Galaxy > instance) looked pretty simple, but maybe I missed something. > > > > First, I modified the universe_wsgi.ini file by removing the "#" before > the tool_config_file and tool_path lines. > > This one step should really be all you need to do (any other files get > created automatically with reasonable defaults if missing) as far as > configuration goes. Did you restart your galaxy instance after editing > universe_wsgi.ini? > > -Dannon

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