Hello again Thomas,
Unfortunately I forgot about your email from last summer - which
was shortly before the GCC2013 conference where we had some
productive discussions about the BLAST+ wrappers, e.g.
Further replies in-line below...
On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas
>> 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.
) 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.
That's done now, and will be in the forthcoming v0.1.0 release of the
Galaxy BLAST wrappers - available for early testing here:
> I think we just need to add another integer parameter under the
> 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?
The BLAST+ wrappers have turned into a team effort, managed from
this GitHub repository: https://github.com/peterjc/galaxy_blast/
On Fri, Jun 14, 2013 at 1:59 PM, Berner, Thomas
We edited the ncbi_blastn_wrapper.xml (attachment) a little bit as you
can see and created a taxid_name.loc file for testing by our own. This
is what we were thinking of in a very simple way. But if the list spreads
out we would like to have textbox for pre-selection above the
drop-down-menu like it is in the "edit Attributes" menu if it is possible...
Now we have an issue tracker for the BLAST+ wrappers, I've filed an
enhancement issue on this with notes from your email - I don't think
the negative filtering by taxid would work though:
If you have a GitHub account you are welcome to subscribe to the
issue and comment there - or reply by email.