New Galaxy Community tool sharing site now available

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New Galaxy Community tool sharing site now available

Greg Von Kuster
Hello Galaxy community,

We have introduced a new Galaxy tool sharing community site at http://usegalaxy.org/community.  The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools.

We hope that you will find this site useful for hosting tools that you would like to contribute and share.

We'll keep you informed as the site's features evolve.

Here is the current information about uploading and downloading tools from the site.

Uploading Tools

Tool File Format

A tool file is a tar-format (bzipped or gzipped tar are valid) archive containing all the files necessary to load the tool in Galaxy. At the very least, it must contain a Tool XML File, and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic instructions below, please include a README file which details these steps. 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). Please do not include precompiled 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, please be sure the license allows for redistribution before including any part of that tool in the tar archive!

There are no requirements about the directory structure inside the tar archive, but for ease of use, it's generally a good idea to put everything inside of a subdirectory, instead of directly at the top level.

Tool File Example

To package up 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 Community 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 the tool has successfully uploaded, you will be redirected to the Edit Tool page. Please 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 easily findable by users looking to solve specific problems. Please 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. Once approved, it will be visible to everyone. At that point, the description and associated categories can only be changed by an administrator.

Once the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, clicking the context menu to the right of the tool's name, and selecting "Upload a new version."


Downloading and Installing Tools

A tool's download link will send you the tool tar archive. Once downloaded, unpack the tool on your local Galaxy instance's server:

    user@host:~% tar xvf galaxy_tool.tar
    ...
    user@host:~% tar zxvf galaxy_tool.tar.gz
    ...
    user@host:~% tar jxvf galaxy_tool.tar.bz2
    ...
    
If the tar archive includes a README file, consult it for installation instructions. If not, follow these basic steps:
  1. Create a directory under galaxy_dist/tools/ to house downloaded tool(s).
  2. In the new directory, place the XML and any script file(s) which were contained in the tar archive.
  3. 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.
  4. Add the tool to galaxy_dist/tool_conf.xml.
  5. Restart the Galaxy server process.

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 managing the tool_conf.xml file by hand. In the meantime, this is the process.



Greg Von Kuster
Galaxy Development Team




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Re: New Galaxy Community tool sharing site now available

Davide Cittaro

On Jul 2, 2010, at 6:45 PM, Greg Von Kuster wrote:

Hello Galaxy community,

We have introduced a new Galaxy tool sharing community site at http://usegalaxy.org/community.  The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools.



Great! Uploading ASAP some stuff!

d

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