[Bio-Linux] Galaxy updates on Bio-Linux

[Tim Booth]

Dear All,

A few people have reported significant issues with Galaxy Server after
upgrading to Bio-Linux 8.  Galaxy is big and complex, has a large number
of dependencies, and is being rapidly developed, so maintaining it on
Bio-Linux is always going to be a challenge.  However I have now updated
the packages and made several modifications and run through various
tests, so I hope that the result, while not perfect, will be a marked
improvement.

In particular, installing tools via the "Tool Shed" should now work
properly.  For example, I've run through the Galaxy 101 at
https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need to
install the "join on genomic intervals" tool from the tool shed.  It
complains it can't auto-install bx_python, but then it works anyway as
bx_python is already in the core Galaxy package.

You can also use the new reference data management features as described
here: http://www.ncbi.nlm.nih.gov/pubmed/24585771
At the moment I've included the UCSC genome importer and the BWA index
builder by default.  Others can be installed via the Tool Shed.

I've also put a new documentation page up at
http://environmentalomics.org/bio-linux-galaxy explaining how Galaxy is
installed on Bio-Linux and how and why this differs from the "standard"
config described on the Galaxy website.

One particular thing I'm still working to address is that Galaxy on
Bio-Linux refuses to import saved histories.  I'm not sure why this is
right now.  Export seems to be OK.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705