February 2013 - galaxy-user - lists.galaxyproject.org

replicates in cuffdiff output
by Johanna Sandgren 19 Feb '13

19 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 14 Feb '13

14 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 14 Feb '13

14 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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Installing new tools from the tool shed
by David Joly 14 Feb '13

14 Feb '13

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. Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox> Finally, I log as the Admin, and select "Search and browse tool sheds", select one tool (trinityrnaseq for example), click "Preview and install" and then "Install to Galaxy". However, that's where I get an error message: The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a <toolbox> tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is <toolbox tool+path="..shed_tools">). Any idea? Thanks, DJ

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Reference Genome in Lastz
by Murphy, Caitlin N 13 Feb '13

13 Feb '13

I'm trying to map a series of short sequencing reads from a clinical isolate of Klebsiella pneumoniae to the Klebsiella pneumoniae MGH 78578 genome which is found on NCBI. This reference genome is not listed under mapping Lastz, which it says I should contact the galaxy team if that is the case. I'm new at all this and trying to upload the reference genome myself, but I am new at all this and any help would be amazing. Thanks, Caitlin Murphy

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Galaxy on one computer not showing latest runs in history
by Dikla Aharonovich 13 Feb '13

13 Feb '13

Hi I am running galaxy and am working both from home and work. Last night at home, my history had up to 35 items in it, that all ran. At work today, I can only see 30. This includes number 27 in my history, which shows that it is still running, while I already saw the results for it at home last night. I tried logging in and out, and pressing the refresh button. Please let me know what else may be causing this Many thanks, Dikla

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hg19 reference gnome for Tophat2
by Sachit Adhikari 13 Feb '13

13 Feb '13

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit

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