February 2014 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 25 Mar '14

25 Mar '14

Hello all, *We are pleased to announce that Early Registration <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and Poster Abstract Submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for the 2014 Galaxy Community Conference (GCC2014) <https://wiki.galaxyproject.org/Events/GCC2014>.* GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *Early registration <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. *Abstract submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Compute an expression
by Hamid Qaedi 07 Mar '14

07 Mar '14

Dear All I have a tabular file and using compute (version 1.1.0) tool under text manipulation menu, I 'm going to do a computation to find rows in which column2 and 3 (c2 and c3) are similar in values (values are A,T,C and G) . It seems the syntax for doing that is "c2==c3", but it dosent work. Can anybody help? Any help would be appreciated. Hamid

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bc-bio galaxy
by JPeden＠tgen.org 03 Mar '14

03 Mar '14

Brad, We are looking for some advice on going from our current Galaxy to the nglims fork of Galaxy you have created. The last post I've seen on the subject of moving to the nglims Galaxy was here: http://user.list.galaxyproject.org/add-nglims-to-galaxy-dist-td4656015.html Is it still the case that it "would best to first try it out on a separate instance before thinking about integrating with your production Galaxy. It does take a bit of tweaking …." ?? Second, when I install the nglims fork of galaxy is there a way to have galaxy use the tools and genomes in bc-bio? On our original install, before we used bc-bio, I added tools mainly via the tool shed. It would be nice be to have galaxy using the same tools. Any other advice would be greatly appreciated. Thanks Jim --

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March 2014 Galaxy Update Newsletter
by Dave Clements 28 Feb '14

28 Feb '14

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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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