July 2010 - galaxy-user - lists.galaxyproject.org

Python error when running Bowtie for Illumina
by Weng Khong Lim 01 Feb '11

01 Feb '11

Hi all, I'm new to next-gen sequencing, so please be gentle. I've just received a pair of Illumina FASTQ files from the sequencing facility and intend to map them to the hg19 reference genome. I first used the FASTQ Groomer utility to convert the reads into Sanger reads. However, when running Bowtie for Illumina on the resulting dataset under default settings, I received the following error: An error occurred running this job: *Error aligning sequence. requested number of bytes is more than a Python string can hold* * * Can someone help point out my mistake? My history is accessible at http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch Appreciate the help! Weng Khong, LIM Department of Genetics University of Cambridge E-mail: wkl24(a)cam.ac.uk Tel: +447503225832

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search in libraries
by Davide Cittaro 18 Aug '10

18 Aug '10

Hi all, how does the library search tool work? I'm trying on the public galaxy but I can't get any result... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Embedabble workflows and automating execution
by Alex Quezada 12 Aug '10

12 Aug '10

Two questions: 1. Is it possible to embed a workflow inside another workflow? 2. Is it possible to run a workflow via command line so that the execution could be automated? Say some other process produces the inputs, then command line or some other API (url maybe?) passes a reference to the inputs and kicks off the workflow. I found this, but no resolution: http://bitbucket.org/galaxy/galaxy-central/issue/43/workflow-command-line-e… ************************************************ Alex Quezada Software Developer Genome Science/Joint Genome Institute (B-6) Bioscience Division MS M888 Los Alamos National Laboratory Los Alamos, NM 87545 phone: (505) 606-2153 fax: (505) 665-3024 email: alexq(a)lanl.gov ************************************************

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Help needed
by Rehman, Atteeq (NIH/NIDCD) [F] 02 Aug '10

02 Aug '10

Hello, I have a list of variants(SNPs) that differ from reference sequence (in my human subject DNA) and I want to filter out the known variants reported in dbSNP, so that I can have a short list of putative novel variants. Could somebody please tell me how can I do this? [cid:image001.jpg@01CB30BC.5FD96A20] Atteeq Ur Rehman Visiting Fellow National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Room 2A-19, 5 Research court, Rockville, MD, USA, 20850. Lab Ph. No. 301-402-9059

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processing GFF3 file of variants
by Paul Webster 02 Aug '10

02 Aug '10

Hello all, I have a GFF3 file of variants from nextgen sequencing and want to find non-synonymous changes. Any suggestions? One possible way would be: 1. Use tool "Compute an expression on every row" to extract the reference allele and sample allele from column 9 (attributes column) of the GFF3 file 2. Download some codons (see help for "mutate codons" tool for more info about this) 3. Use the "mutate codons" tool to mutate the codons with the variants extracted from the GFF file. Here is the problem:- The help examples for the tool "compute an expression on every row" are very simplistic. This tool is much more powerful. Where can we find information about how to extract substrings with this tool?

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Re: [galaxy-user] Eucalyptus genome in Galaxy
by Reddy.Thumma＠csiro.au 29 Jul '10

29 Jul '10

Hi, Could you please include Eucalyptus genome (http://eucalyptusdb.bi.up.ac.za/) in the public version of Galaxy. It is being sequenced at JGI and recently 8x assembly was completed. Thank you, Regards, Bala Thumma

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Iterating over a set of files
by Alex Quezada 28 Jul '10

28 Jul '10

Hello, I have a use case where the input to the workflow would be a directory (local to Galaxy instance) with a variable number of files in it. The workflow should iterate over all the files, running the workflow for each one sequentially. How would I got about doing this in galaxy? It's easy enough to write an input tool that takes a directory and outputs the files, but not sure how to make it iterate. Any ideas? ************************************************ Alex Quezada Software Developer Genome Science/Joint Genome Institute (B-6) Bioscience Division MS M888 Los Alamos National Laboratory Los Alamos, NM 87545 phone: (505) 606-2153 fax: (505) 665-3024 email: alexq(a)lanl.gov ************************************************

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July 26, 2010 Galaxy Development News Brief
by Greg Von Kuster 26 Jul '10

26 Jul '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Galaxy Tool Shed now includes the ability to upload an archive consisting of a suite of tools in addition to a single tool archive
by Greg Von Kuster 22 Jul '10

22 Jul '10

Hello Galaxy Community, The Galaxy Community Space has been renamed to be the Galaxy Tool Shed ( contributed by Dave Clements ), the location is still http://usegalaxy.org/community. The site now includes the ability to upload an archive consisting of a suite of tools in addition to a single tool archive. Here is the information about uploading both of these types of archives. Please start sharing tools, and let us know if you encounter any problems. Also, let us know what new features you would like to see in the tool shed. Our next update will include the ability to rate tools. Creating an archive containing a tool or a suite of tools A tool or tool suite archive is a tar-format file (bzipped or gzipped tar are valid) containing all the files necessary to load the tool(s) into a Galaxy instance. Tool Suite Archive A tools suite must include a file named suite_config.xml which provides information about the id, name, version and description of the tool suite, as well as the id, name, version and description of each tool in the suite. Here is an example suite_config.xml file. <suite id="lastz_toolsuite" name="Suite of Lastz tools" version="1.0.0"> <description>This suite contains all of my Lastz tools for Galaxy</description> <tool id="lastz_wrapper_2" name="Lastz" version="1.1.0"> <description> map short reads against reference sequence</description> </tool> <tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> <description> map short paired reads against reference sequence</description> </tool> </suite> New versions of the suite can be uploaded, replacing an older version of the suite, but the version attribute of the tag must be altered the same way that the version attribute of a single tool config must be altered if uploading a new version of a tool. The id, name and version attributes of each tag in the suite_config.xml file must exactly match the same attributes in each associated tool config in the archive or you will not be allowed to upload the archive. In addition to the suite_config.xml file, the archive must include all tool config files, executables, functional test data (if your tool config includes functional tests) and other files needed for each of the tools in your suite to function within Galaxy. See the information about single tool archives below for additional hints to enable ease-of-use when others download your suite of tools. For example, to package the above Lastz suite of tools: user@host:~% tar jcvf ~/Desktop/galaxy_lastz_toolsuite.tar.bz2 lastzsuite lastzsuite/ lastzsuite/README lastzsuite/suite_config.xml lastzsuite/lastz_paired_reads_wrapper.py lastzsuite/lastz_paired_reads_wrapper.xml lastzsuite/lastz_wrapper.py lastzsuite/lastz_wrapper.xml lastzsuite/lastz-distrib-1.02.00/ lastzsuite/lastz-distrib-1.02.00/src/ lastzsuite/lastz-distrib-1.02.00/src/Makefile lastzsuite/lastz-distrib-1.02.00/src/version.mak lastzsuite/lastz-distrib-1.02.00/src/lastz.c lastzsuite/lastz-distrib-1.02.00/src/lastz.h ... ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. Single Tool Archive A single tool archive must include a tool config file and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic instructions below, include a README file to provide details. If the tool (or parts of it) are written in C, the source code can be included (or put links to the source in the README). Do not include pre-compiled binaries without source since Galaxy is run on a wide variety of platforms. Also, if you are only wrapping or providing a Galaxy config for a tool that is not your own, be sure the license allows for redistribution before including any part of that tool in the archive. There are no requirements about the directory structure inside the archive, but for ease of use it's generally a good idea to put everything inside a sub-directory, instead of directly at the top level. For example, to package the Lastz tool's config file, Galaxy wrapper, and the C source: user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz lastz/ lastz/README lastz/lastz_wrapper.py lastz/lastz_wrapper.xml lastz/lastz-distrib-1.02.00/ lastz/lastz-distrib-1.02.00/src/ lastz/lastz-distrib-1.02.00/src/Makefile lastz/lastz-distrib-1.02.00/src/version.mak lastz/lastz-distrib-1.02.00/src/lastz.c lastz/lastz-distrib-1.02.00/src/lastz.h ... ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. Editing Information, Categories, and Submitting For Approval Simply uploading a tool to the Galaxy too shed will not allow other users to find and download your tool. It will need to be approved by an administrator before it appears in the tool list. After your archive has successfully uploaded, you will be redirected to the Edit Tool page. Provide a detailed description of what the tool does - this will be used by administrators to understand the tool before approving it for display on the site. Once approved, this information will be displayed to users who view your tool. In addition, the site administrators will have configured a number of categories with which you can associate your tool to make it easy to find by users looking to solve specific problems. Associate as many categories as are relevant to your tool. You may change the description and associated categories as often as you'd like until you click the "Submit for approval" button. Once submitted, the tool will be approved or rejected by an administrator. If the tool is rejected, you will see information about why it was rejected, and you can make appropriate changes to the archive and re-submit it for approval. When it is approved, your archive will be visible to everyone. At that point, the description and associated categories can only be changed by an administrator. When the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, clicking the "Tool actions" menu in the upper right corner of the page, and selecting "Upload a new version" from the menu. Downloading and Installing Tools A tool's download link will send you the tool archive. Once downloaded, unpack the tool on your local Galaxy instance's server: user@host:~% tar xvf galaxy_lastz_tool.tar ... user@host:~% tar zxvf galaxy_lastz_tool.tar.gz ... user@host:~% tar jxvf galaxy_lastz_tool.tar.bz2 ... If the archive includes a README file, consult it for installation instructions. If not, follow these basic steps: Create a directory under galaxy_dist/tools/ to house downloaded tool(s). In the new directory, place the XML and any script file(s) which were contained in the archive. If the tool includes binaries, you'll need to copy them to a directory on your $PATH. If the tool depends on C binaries but does not come with them (only source), you'll need to compile the source first. Add the tool to galaxy_dist/tool_conf.xml. Restart your Galaxy server process. In the near future, we plan to implement a more direct method to install tools via the Galaxy administrator user interface instead of placing files on the filesystem and manually managing the tool_conf.xml file. Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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microarray analysis tools
by Leandro Hermida 21 Jul '10

21 Jul '10

Hello, Are there publicly available tools in Galaxy for microarray data analysis, visualization, etc? Or is this kind of GenePattern's space and you want to stay separate? :) best, Leandro

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