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 * Egg Update: boto 2.2.2  * Egg Update: [[https://github.com/boto/boto|boto]] 2.2.2

March 12, 2012 Galaxy Development News Brief

Get Galaxy


new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist

upgrade: % hg pull -u -r 40f1816d6857

Important Changes to Tool Organization

The Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release (not this one). Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised "Migrating tools" section of the Galaxy tool shed wiki to understand how this process will work:

tool shed

Migrating tools from the Galaxy distribution to the Galaxy Main tool shed

In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more...

XML configuration files used to populate your Galaxy tool panel

In the past, the file named by your tool_config_file configuration setting in your universe_wsgi.ini file was the only file used to populate your Galaxy tool panel. The default name for this file is tool_conf.xml. Since this was the only file involved in populating your Galaxy tool panel, it defined the items (tools, workflows, sections and labels) that would be displayed and the way in which they would be arranged. Read more...

Managing the layout of your Galaxy tool panel

The 3 or more files described in the previous section (tool_conf.xml, one or more shed_tool_conf.xml files, and migrated_tools_conf.xml) are all used to load tool panel items (tools, sections, labels and workflows). A new file named integrated_tool_panel.xml has been introduced to define the arrangement for displaying these loaded items in your Galaxy tool panel. Read more...

Galaxy Tool Versions

When included in the Galaxy distribution, tools are defined by "id" and "version", among other attributes. For example, the filter tool has id="Filter1" and version="1.1.0". When installed from a tool shed, the tool's id becomes its "guid" attribute from the tool shed. If it is migrated from the Galaxy distribution to the tool shed, the filter tool will have the guid: "toolshed.g2.bx.psu.edu/repos/devteam/filter/Filter1/1.1.0". To provide backward compatibility for Galaxy workflows and the rerun button in a Galaxy history item, a mapping between the tool's old id and version and its new id (guid) is provided by building a chain of relationships between tool versions. This happens automatically for every tool that is loaded into your Galaxy instance. Read more...

1) When an installed tool shed repository that includes tools is being reinstalled, allow the admin to select a different section in the tool panel (than was originally selected when the repository was last installed) to contain the included tools.

2) Load proprietary datatypes from installed tool shed repositories before the datatypes in the Galaxy distribution are loaded. We do this because the distribution includes some extremely generic sniffers (eg text,xml) which will catch pretty much anything, making it impossible for proprietary sniffers to be used. Proprietary datatypes contained in installed repositories are loaded in order of oldest installation first, followed by next oldest installation, etc. In handling conflicts (2 different datatypes that use the same extension), the rule is that a datatype currently being loaded will always override a conflicting datatypes that was previously loaded. Since datatypes defined in Galaxy's datatypes_conf.xml file are loaded last, they will override conflicts that may occur if tool shed repositories that contained datatypes were installed. If a new tool shed repository is being installed into a running Galaxy instance, conflicting datatypes will not override those currently in the datatypes registry.

1) Fix for rendering the page that allows you to select a tool section in which to include tools contained in a repository installed from a tool shed where the tool panel include tool section labels.

New tool shed features

1) Chain Galaxy tools into a lineage of tool versions. This enables workflows and the rerun button on history items to work when a new version of a tool is loaded into the Galaxy tool panel. Version information for tools included in tool shed repositories is maintained for each changeset revision in the tool shed, and this information can be retrieved from the Administrative "Manage installed tool shed repositories" menu item for installed tool shed repositories that contain tools. This new functionality eliminates the need for the tool_id_guid_map table and associated features, so they have all been removed. See the section in the Galaxy tool shed wiki for details (listed above as well): Galaxy Tool Versions

2) Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel.

New & Updated Tools

Many tools have been recently upgraded. Please review Admin/Config/Tool Dependencies for these and other recently updated Tool Dependencies. Please see Galaxy's Main Tool Shed for additional new tools.

  • RNA-Seq Tools

    • Added CuffMerge version 1.0.0

      • Requires helper script: gtf_to_sam version 1.3.0

    • Updates for Cufflinks/compare/merge/diff tools

      • Modified default parameter values on tool form
      • Improved error message when bias correction/sequence data cannot be used
  • Updates for TopHat

    • Remove maximum value for TopHat parameter initial_read_mismatches

  • Added RViewer external display application

  • Updated IGV external display application, so that displays using vcf_bgzip will now maintain vcf headers

Galaxy Track Browser (GTB)


  • New:

    • Enable visualization of ENCODE peak tracks (see graphic below)

    • Dynamic filtering of read tracks using quality scores
    • Enable toggling between groups of individual tracks and composite tracks
    • Enable Composite Tracks to be saved and restored
    • Make track min and max values editable inline
    • Save and restore track/group filters and tool state
  • Bug fixes:

    • Clear reference track when changing chromosomes
    • To only show differences if reference data is available
    • Use sum rather than mean for data aggregation in BBIDataProvider
    • Indicate changes when config values are changed or items are reordered or grouped
    • Move 'more rows' icon from tile level to track level

Trackster visualization of ENCODE and Composite Track data using dynamic filters



            #{inputs_file_variable | option 1 | option n}
                 input_file_variable = is the name of a module input variable
                 |  = the delimiter for added options. Optional if no options.
                 options = basename, upper, lower
                 basename = keep all of the file name except the extension
                            (everything before the final ".")
                 upper = force the file name to upper case
                 lower = force the file name to lower case
            #{input1 | basename | upper}

User Interface (UI)

Data and Libraries




galaxy-cental, galaxy-dist

Bug Fixes




March 2012 Galaxy Update

GCC2012 Update

2012 Galaxy Community Conference

Training Day

Galaxy is Hiring!

Galaxy wants YOU
The Galaxy Team Wants You!
Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring. Read more...

About Galaxy


The GalaxyTeam is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.

Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State, and Emory University.

Join us at Twitter @galaxyproject or just read our tweets Galaxy on Twitter

Jennifer Jackson, Galaxy Team. Posted to DevNewsBriefs on <<XXXXX>>