Excellent. Thanks, Jeremy! -b On Fri, Jul 20, 2012 at 8:37 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Brian,
For the initial trinity de novo assembly, I took Jeremy's initial workflow and tweaked it to work with the latest release - and submitted it to the galaxy tool shed.
Excellent. I'll remove my old Trinity wrapper from our code base and point people to your wrapper.
There are some complexities here, such as not knowing ahead of time how many different samples are to be processed - so this needs to be determined dynamically, which impacts the overall complexity of the total workflow. Is this possible in Galaxy, and if so, are there examples I can work from?
Take a look at the repeat element; it enables a user to specify a number of inputs to a tool.
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crepeat.3E_t...
Tool wrapper that use the repeat element include the GATK's depth of coverage and Cuffdiff.
Best, J.
-- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas