Thanks! This looks very useful for me. I'm also interested in fleshing out the 
wrapper, (implementing all possible options, like bowtie's <<full parameter 
list>>), but this should fit my purposes for now.

Best regards,
Patrick

Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Gesendet: Freitag, 18. Januar 2013 04:37
An: Sorn, Patrick
Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu'
Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy

I have a very basic STAR wrapper that works:

https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default

For now, the wrapper does two things: maps RNA-seq reads and identifies 
chimeric reads/junctions. There are tons of options that aren't yet 
implemented, but the basics are there.

Eventually I'll put the wrapper in the toolshed, but if you want to use it now, 
you'll need to create your own star_indexes.loc table (identical in structure 
to the bowtie_indexes.loc table) and add the appropriate entry to 
tool_data_table_conf.xml This page explains the details of these files:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If you're interested in helping to flesh out the wrapper, pull requests or 
patches are welcome.

Thanks,
J.



On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote:


Hi all,

I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if 
anyone else is working on this? If nobody is, I would do this.

Best regards,

Patrick Sorn
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