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.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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
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