On Mon, Feb 4, 2013 at 6:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang <yangluob@isu.edu> wrote:

...

Hi, Peter,

What difficulties did you see to include psi-blast and phi-blast when you were working on the other programs in the NCBI+ suite? I would be interested in creating a tool configuration file for each of these two.

Thanks, Luobin

Hi Luobin,

At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't look too different for wrapping. We would need to define a third loc file for the RPS BLAST domain databases (like the existing loc files for nucleotide and protein databases).

I've got wrappers working for rpsblast and rpstblastn with a new blastdb_d.loc file for the associated domain databases, currently in my bitbucket repository and live on our internal Galaxy server. Barring any unexpected problems, I'll include this in an update to the Tool Shed in a week or so - so watch this space: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ Meanwhile work on wrapping psiblast is ongoing, with several contributors. We'll need to have ASN.1 base formats defined in Galaxy first (discussed on another thread). Regards, Peter