Hi All,

That (fubar in testtoolshed) star wrapper was derived from one originally
written by Jeremy Goecks. I modified it for multiple inputs and added a few
tweaks and it has been in production use in our group for about 6 months so
I'm pretty sure it works reasonably well in our hands at least.

I would really appreciate any available help getting it to a proven useful
state - suggestions and code welcomed. I have not moved it to the main
toolshed because aside from some encouragement, I've had no feedback to
suggest it's working - or not. It is extremely fast - we regularly see
200-300M reads per minute in the logs!

We regularly run a whole experiment worth (eg 12 - 24) fastq files
simultaneously with the shared memory option working on our cluster - see
the readme.

Star index files made with a gene model (requires valid gff3) are huge -
20-30GB for hg19 - hence the need for shared memory if you run multiple
jobs. That will eventually become a serious problem if you really want to
allow users to make their own - we definitely do not. You need to be very
careful about matching the gene model gff3 file to the reference and I had
enough trouble getting it right for the few major genomes we use to make me
think that I do not want users trying to do that generating 25GB of rubbish
every time they get it wrong.

There are challenges to do with needing different indexes for different
length reads but we are seeing fairly consistent 60bp single ended reads
for most of the incoming RNA seq experiments.

A data manager would be a boon if anyone cares to write one...


On Thu, Sep 25, 2014 at 6:55 AM, Curtis Hendrickson (Campus) <
curt...@uab.edu> wrote:

> Bjorn
>
> We'd be interested in this tool, as well. Any idea how close to functional
> it is?
> I see it's only on TEST toolshed, and not on production, at this point.
>
> I don't see any related Trello card when searching on "star"
>
> Regards,
> Curtis
> Galaxy Admin @ University of Alabama at Birmingham
>
> -----Original Message-----
> From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn Grüning
> Sent: Wednesday, September 24, 2014 3:15 PM
> To: galaxy-dev@lists.bx.psu.edu; hoove...@helix.nih.gov >> David Hoover
> Subject: Re: [galaxy-dev] tool for STAR RNA-seq aligner
>
> Hi David,
>
> yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I
> think Ross has done some work on it.
> The main problem with Star is that is needs special indices (and a lot of
> it) and it would be great to offer data managers for it.
>
> Cheers,
> Bjoern
>
> Am 24.09.2014 um 22:05 schrieb David Hoover:
> > Hi,
> >
> > I am developing a tool for STAR (https://code.google.com/p/rna-star/),
> and I realize I may be reinventing another wheel.  Has anyone else created
> a tool for STAR?  There's nothing else in the toolsheds for it yet.
> >
> > David
> >
> > --------------------
> > David Hoover, PhD
> > Helix Systems Staff
> > SCB/DCSS/CIT/NIH
> > 301-435-2986
> > http://helix.nih.gov
> >
> >
> >
> >
> >
> > ___________________________________________________________
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