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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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Rhesus Macaque genome in lastz
by Lakshmanan Iyer 20 Jul '10

20 Jul '10

Hi In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque genome. The web site says: "If your genome of interest is not listed, contact the Galaxy team" Could you please make this reference genome available? Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly -best -Lax

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Swine genomes for NGS tools
by Kelly Vincent 20 Jul '10

20 Jul '10

Jeff, Two swine genomes have been added to the NGS tools. These are the build 9.58 you specifically requested (listed as Scrofa9.58) and also the susScr2 (Nov. 2009, available from UCSC). Let us know if you run into any problems using either. Regards, Kelly

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problems accessing the data
by research pal 20 Jul '10

20 Jul '10

Dear galaxy, I am not able to get the requisite output when I try the option with the output format "selected fields from primary and related tables" which then asks me to customize from the hg18.KgXref fields. The error message that I am getting is "Can't find route from wgEncodeBroadChipSeqPeaksHmecCtcf to kgXref via all.joiner ". Could you please help ? warm regards, Amit.

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Galaxy Developer Conference 2011
by Anton Nekrutenko 19 Jul '10

19 Jul '10

Dear members of Galaxy Community: We are starting to prepare for the Second Galaxy Developer Conference in 2011. This time we would like to hold it in Europe and we were asked to consider Uppsala and Heidelberg. However, Galaxy is a community project and we would like to ask you for input. If any of you knows good and reliable conference facility, please let us know. We will then research this and finalize the conference planning. So let us know... Thanks, anton + galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Re: [galaxy-user] [galaxy-bugs] Galaxy tool error report from azovoil@gwdg.de
by Jeremy Goecks 18 Jul '10

18 Jul '10

>> >> Error: this SAM file doesn't appear to be correctly sorted! >> >> >> Could you please add also the function from cufflinks for sorting sam file before use? > > Given that you're not using Tophat to map your reads, you'll want to sort your reads before uploading them to Galaxy b/c Galaxy does not (yet?) have a tool to sort SAM files. [cc'ing galaxy-user as this may be useful information to other users.] Hi Zovoilis, I was mistaken in writing that Galaxy cannot sort SAM files. Galaxy can sort SAM files; here is an example history that illustrates the sorting of a SAM file: http://test.g2.bx.psu.edu/u/jeremy.goecks/h/sorting-sam-file-for-cufflinks There are two steps in sorting a SAM file: (1) removing SAM headers via the 'remove lines from beginning of a file' tool and (2) using the 'sort data in ascending or descending order' tool to sort by chromosome name and then by position. Samtools provides a single-step process for sorting SAM files, and we expect to add this capability to Galaxy in the future so that the above 2-step process can be replaced by this single step. Best, J.

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July 16, 2010 Galaxy Development News Brief
by Greg Von Kuster 16 Jul '10

16 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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microRNA Seq data workflow analysis
by Ana Sevilla 15 Jul '10

15 Jul '10

Dear Galaxy users. I would like to use Galaxy software for my microRNA data analysis. Could someone share with me the workflow I should use? Thank you very much in advance. Ana * * -- Ana Sevilla Hernandez Mount Sinai School of Medicine. 1425 Madison Ave. (Icahn Building) Floor 13. Room 26 Phone: (001) 212 659 8251 E-mail: Ana.Sevilla(a)mssm.edu

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Fwd: Install local copy of GALAXY
by Anton Nekrutenko 14 Jul '10

14 Jul '10

Begin forwarded message: > From: "Phang, Tzu" <Tzu.Phang(a)ucdenver.edu> > Date: July 14, 2010 4:09:40 PM EDT > To: "anton(a)bx.psu.edu" <anton(a)bx.psu.edu> > Subject: Install local copy of GALAXY > > HI ANTON, > > Great GALAXY discussion session at ISMB2010 in Boston. Our sequencing core lab is very interested in installing a local copy of GALAXY for our analysis needs. Could you lead me to the right direction about where I should start? > > Thanks > > Tzu Lip Phang PH.D > Assistant Professor > > Division of Pulmonary Sciences and Critical Care Medicine > University of Colorado Denver > Anschutz Medical Campus > Research 2, Box C272, 9th Floor > 12700 East 19th Avenue > Aurora, CO 80045 > > Office: 303-724-6057 > Fax : 303-724-6042 > Cell : 720-635-6323 Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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