Galaxy
DevNewsBriefs/2011_05_20

May 20, 2011 Galaxy Development News Brief


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GCC 2011

May 24-26, 2011 Galaxy Community Conference, Lunteren, The Netherlands.


What's New

NBIC Galaxy Hackathon Results

Two new features (so far) were created and added to Galaxy from the May conference.

Hackaton: tool_conf.xml Autogeneration

Work from the NBIC Galaxy Hackathon by Rob Hooft, Henk van den Toorn, and Wil Koetsier which adds new optional tags to tool configuration files, and a script which uses these tags to automatically generate tool_conf.xml.

The scripts can be found at:

Documentation on the new XML tags and how to use the scripts has not yet been prepared.

Hackathon: Tool Tags

Work from the NBIC Galaxy Hackathon by Freek de Bruijn, Alex Bossers, and Nate Coraor which enables associating tags with tools. This feature requires 'enable_tool_tags = True' since there are some inefficient database operations performed during tool loading to support this feature.

Tool authors can specify tags directly in tool configuration files with the new optional <tags> tagset:

  <tags>
    <tag>ngs</tag>
    <tag>mapping</tag>
  </tags>

If used with the tool_conf.xml autogeneration scripts, this will create <tool> tags containing a new "tags" attribute:

Upon startup, Galaxy associates these tags with the tools and presents them in a cloud at the top of the tool menu when unhidden via the tool panel's "Options" menu.

Picard

http://picard.sourceforge.net

New Galaxy tools wrapping the most commonly used Picard functions related to metrics and repair of mapped short read sequencing.

Metrics include

Repair tools include

FastQC

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

New tool wrapper generates a comprehensive and useful QC report.

Inputs and Outputs

2011_05_20_fastqc.png

Workflows & Multiple datasets

Workflows can now be run on multiple datasets at the same time. The run workflow page will now show a new stacked dataset icon.

2011_05_20_workflow1.png

Upon clicking that, the selection box changes to a multi-select, and an independent workflow execution will occur for each of these input dataset steps. The rest of the parameters of the workflow will be identical. Combining this functionality with the existing "Send results to a new history" option will send the results of *each* workflow execution to a separate history, numbered sequentially "<name> 1", "<name> 2", etc., where <name> is whatever text you put in the new history name box.

2011_05_20_workflow2.png

Please note that this new type of "multiple-input dataset" step can currently be used only once in any individual workflow.


Updated & Improved

Current Tools

New Tools

Trackster

User Interface (UI)

CloudMan

2011_05_20_cloudman1.png

Source

pre-defined by the Galaxy framework. Some of these already existed but were undocumented. All have been changed to use a common (pythonic) naming scheme, but the old names are retained for backwards compatibility:

Tool Framework

Test Framework

Bug Fixes


About Galaxy

The Galaxy team 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.

GalaxyTeam

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last edited 2016-09-22 07:32:48 by DaveClements