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/
___________________________________________________________ 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/
