Hi,

Am 24.09.2014 um 22:39 schrieb David Hoover:
Why didn't I see these before?  Hmm, I thought I had searched both toolsheds...

I was kind of hoping someone had tackled this in a different way.  It would be 
nice if there was a composite datatype for the reference genome.  It is 
important for users to generate their own personal genome references, rather 
than rely on shared, admin-installed indices.  And you're correct, we'd need at 
least 5-10 separate genome references for each organism, depending on read 
length and annotation GTF.

Yes :( For me this was to cumbersome and I decided to wait until the TopHat successor will be released :)

Back to wheel reinvention.

BTW, can you tell me which standardly installed tools use composite datatypes?  
It's always easier to build thing from comparison, rather than from scratch.

Sure. Have a look at the Galaxy wrappers from Peter: https://github.com/peterjc/galaxy_blast

Galaxy Datatypes are composite.
Cheers,
Bjoern

David

--------------------
David Hoover, PhD
Helix Systems Staff

On Sep 24, 2014, at 4:14 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

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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