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September 07, 2012 Galaxy Development News Brief

Get Galaxy


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

upgrade:  $ hg pull -u -r e6444e7a1685 

BLAST+ Migration

The tool set NCBI BLAST+ has moved from the Galaxy distribution to the Galaxy Main Tool Shed.

Migration scripts will run upon Galaxy's first launch (after updating to this release) that will automatically handle installing BLAST (and blastxml) from the Tool Shed.

Reference Genome rsync Server

If you would like to obtain the same reference genome builds and indexes as available on the public Galaxy Main instance, these can retrieved from the rsync server at:


For example, to download the complete directory for the 'phiX' genome:

$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .

Genomes are organized in directories by the dbkey. If you are not sure of the dbkey, check your datasets. The dbkey is what is populated into the "database" attribute for a dataset. Read more about how this fits into data integration or setting up native genome indexes.

More Updates to Output and Error Handling

As reported in the July 20th, 2012 News Brief, several changes have been made to the underlying code that determines run result state from tool exit codes and output. There are now additional enhancements to applying regular expressions and exit code checks. Read more...


Admin/Config/Tool Dependencies

User Interface (UI)

  • Enhancements

    • Does not use enable_tracks or enable_pages options anymore; visualizations and pages are enabled for all instances.

  • New

    • Addition of interactive phylogenetic tree visualization.


Galaxy Track Browser (GTB)




$ sh run.sh --daemon/sh run.sh --stop-daemon


Tool Shed

Tool Shed

<tool_shed name="My local tool shed" url="http://localhost:9009/"/>

Now the above entry still works, but the following entry is also ok (notice the '/' character after the port number in the url is no longer necessary):

<tool_shed name="My local tool shed" url="http://localhost:9009"/>




Bug Fixes



News, August and September 2012 Galaxy Updates

September 2012 Galaxy Update


Swiss Galaxy Day

Swiss Galaxy Day

The 1st Swiss Galaxy Workshop will be held October 3-4 in Bern, and is aimed at Galaxy administrators and users alike. We also welcome participants who are using other workflow management systems, and tool developers who are looking for such systems to offer their tools to a wider audience.

We would like to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research.

The workshop is part of the SyBIT Tech Day series.

Who's Hiring

Please Help!  Yes you!
The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it the next Galaxy Update and News Brief.

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.

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