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. http://wiki.galaxyproject.org/Events/GCC2013/BoF Further replies in-line below... Peter wrote:
On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <thomas.berner@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.
That's done now, and will be in the forthcoming v0.1.0 release of the Galaxy BLAST wrappers - available for early testing here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
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
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 <thomas.berner@jki.bund.de> wrote:
Hi Peter,
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...
Regards,
Thomas
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: https://github.com/peterjc/galaxy_blast/issues/36 If you have a GitHub account you are welcome to subscribe to the issue and comment there - or reply by email. Regards, Peter