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.goecks@emory.edu]
Gesendet: Freitag, 18. Januar 2013 04:37
An: Sorn, Patrick
Cc: 'galaxy-dev@lists.bx.psu.edu'; 'dobin@cshl.edu'
Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
I have a very basic STAR wrapper that works:
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:
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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