- galaxy-user - lists.galaxyproject.org

Galaxy + user program unable to locate files
by do kadya 27 Feb '14

27 Feb '14

Hi, Thank You for your kind reply. I am having problem in running command in Galaxy. my current command: <tool_name> <file_having_multiple_file_name_tab_delimited.txt or .tab> <file1.bam> <file2.bam> /usr/bin/x_tool fileList.tab file1.bam file2.bam I have created xml file so that i can run this command through Galaxy. Its showing error: Can't call method "print" on an undefined value at /usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110. When I am running same command from terminal, its working. >From these I have hypothesize: - Galaxy is having different path to run its script, and different file name. - FileList.tab contains list of other files which present in same folder. - As tool is not able to search those files, may be galaxy is having different path where it run the command. ------- While uploading file, I am using user defined path so that galaxy will not create replica of it, hence when I see error file of Galaxy output (by clicking on (i) symbol ) its showing the same path where all my files are located.

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processing multiple files
by mark.rose＠syngenta.com 27 Feb '14

27 Feb '14

Hello Is there a approved way to configure or otherwise use galaxy to process multiple files with a tool or workflow? Using FASTQ Groomer on dozens of files individually is excruciating. Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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large data to upload problem
by do kadya 26 Feb '14

26 Feb '14

Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself. As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me. Some option like tell Galaxy about extension and properties of file, so that it should not replicate. By command line 'x' is working fine. Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan dokadya(a)gmail.com

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RNA-seq work flow does not work
by Alejandro Colaneri 26 Feb '14

26 Feb '14

I'm trying to run the attached workflow to run tophat followed by cuffdiff. But when I hit run a message saying server error appears and that is all (see screen shot attached). I have not clue where the error can be. It appear a very simple work flow. I will appreciate if someone give an idea of what can be wrong. Alejandro

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Variant annotation in galaxy
by garzetti 25 Feb '14

25 Feb '14

Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history? Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history. Any other suggested tool I can use? Thanks! Debora

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Converting VCF to gd_genotype
by Mike Montague 25 Feb '14

25 Feb '14

I'm interested in using the Genomic Diversity tools. I've used these with success for a previous project. For this current project, I've converted a vcf file (29 subjects) to a gd_genotype file. When I attempt to specify individuals, the checkboxes for each subject are not present. Without specifying individuals, I am unable to complete other analyses (overall FST, etc.) I cannot distinguish a difference between the vcf files that were successful from the previous project and this current project's vcf, but I assume there is a format difference that I cannot detect. I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 22:09:49 2014 (UTC). I can share the histories of the projects if necessary. Mike -- ____________ Michael J. Montague, Ph.D. Post-Doctoral Research Associate The Genome Institute, Washington University School of Medicine 4444 Forest Park Avenue, Campus Box 8501 St. Louis, MO 63108 T. 718.809.4093 ____ This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.

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upload more than 2GB data from local computer to local installation of galaxy
by do kadya 25 Feb '14

25 Feb '14

Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says "Connection established, waiting for welcome message" and after some time

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matlab + galaxy
by do kadya 24 Feb '14

24 Feb '14

Hi, How can I call Matlab command in Galaxy ? I refer this link, but don't know how to use it. https://wiki.galaxyproject.org/HelpOnParsers?action=fullsearch&context=180&… I am learning Galaxy, hence don't know much about it. Can i write that command in xml file to integrate it as tool ? I am using below website to create xml files for Matlab. Is it good website to create xml files ? http://cli-mate.lumc.nl/define# Waiting for positive reply.

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Read simulator
by garzetti 22 Feb '14

22 Feb '14

Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora

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Re: [galaxy-user] CummeRbund - biological replicates problem
by Jennifer Jackson 21 Feb '14

21 Feb '14

Hi Tania, Yes, you are correct, the count files only address a portion of the new features. Recent updates to the underlying tools in the Tuxedo suite have resulted in issues of this sort as well (among others). The current plan is to continue with development to enhance the tool wrappers in Galaxy to support as much downstream analysis as practical. I created a new ticket as a catch-all to address this need in a global way. Details will be added as work progresses. https://trello.com/c/ugu8dty0 This is a timely and important inquiry. Our user & development community feedback is an important component in how work is prioritized. _/I encourage you and others interested in this enchantment to "up-vote" the ticket/__/in Trello./_ Comments are also welcome. Trello help: https://wiki.galaxyproject.org/Issues Best, Jen Galaxy team On 2/18/14 5:45 AM, Dottorini, Tania wrote: > Hi Jennifer, > > Thanks for your help, I did my Cuffdiff runs on 2/12/2014 but still I was not able to analyse replicates by CummerBund. The output of replicates(cuff) is empty. > > Thank you > Tania > -- Jennifer Hillman-Jackson http://galaxyproject.org

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