Hi Peter, Nice work. We are working on some general tool wrappers as well (blat, mummer, etc) which have the same difficulty of lots to maintain if something changes...So I also follow your thread on the shared XML parts with great interest.
Regarding the blast xml to table. Its already in your distribution for megablast at metag_tools/megablast_xml_parser.xml there is also a basic wrapper for megablast. Keep up the good work! Alex
-----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Peter Verzonden: dinsdag 28 september 2010 16:07 Aan: James Taylor CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
On Tue, Sep 21, 2010 at 4:35 PM, Peter peter@maubp.freeserve.co.uk wrote:
On Tue, Sep 21, 2010 at 4:14 PM, James Taylor james@jamestaylor.org wrote:
(I'd love to see a complete set of wrappers for NCBI blast+, which we could include with our cloud images right away). Thanks!
I'm working on it - we want to use it on our local server too.
I have a blastplus branch here, currently just minimal wrappers for blastn and blastp: http://bitbucket.org/peterjc/galaxy-central
Early feedback is welcome - I'd like this to follow Galaxy conventions and be taken up as part of the default installation.
Before I do lots of work defining most of the parameters, I started a thread asking how to share definitions between wrapper XML files: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003371.html
I've also written and wrapped a very simple script to split a FASTA file into records with and without BLAST hits - something I plan to use in some simple workflows later on.
I plan to add BLAST ASN1 as a new format, and wrap the blast_formatter application added in BLAST 2.2.24+ to turn this into blastxml, plain text, tabular etc.
There are other things I'd like to add like blastxml to tabular conversion. In this case I'd like to use the Biopython BLAST XML parser - is adding Biopython as a Galaxy dependency going to be a problem? You already have numpy which is the main dependency of Biopython (there are others - all optional).
Regards,
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev