The wrapper isn't set up to support gzipped FASTQ because Galaxy unzips datasets when they are uploaded, so the wrapper won't ever see a gzipped FASTQ dataset. We plan to dataset gzip support to Galaxy in the future.

J.

On Jan 18, 2013, at 10:21 AM, Sorn, Patrick wrote:

Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like?
 
Thanks,
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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