Re: [galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one task
On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas
<thomas.berner(a)jki.bund.de> wrote:
Hi guys,
We recently installed NCBI BLAST + to our local Galaxy instance and now we
need to provide the possibility to filter/mask … by taxon id (taxid) using
the command line option (-window_masker_taxid) of BLAST (cf.
http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be
performed in one task.
However searching in the documentation and the mailing list, I did not find
anything about this.
So it would be great to provide the possibility to subselect by taxid (e.g.
NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the
BLAST integration.
We believe this could be of common interest. It would be great if anybody
could comment on this.
Thanks a lot, Thomas
Hi Thomas,
Full support allowing making your own database with taxid
support will be more complicated - but using databases setup
via the *.loc file (e.g. a downloaded copy of the NR database)
ought not to be too complicated. I think we just need to add
another integer parameter under the advanced options to
set the -window_masker_taxid value. Would that be enough
for your needs?
I wrote the NCBI BLAST+ wrappers but this is starting to
turn into a team effort. There is a lot of other work in progress
on extending the Galaxy BLAST+ wrappers further - I'm
setting up a meeting with the other people already working
on this during the GCC2013 - perhaps this should be a listed
BoF session?
http://wiki.galaxyproject.org/Events/GCC2013/BoF
Regards,
Peter