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!
Van: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:firstname.lastname@example.org]
Verzonden: dinsdag 28 september 2010 16:07
Aan: James Taylor
Onderwerp: Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
On Tue, Sep 21, 2010 at 4:35 PM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
On Tue, Sep 21, 2010 at 4:14 PM, James Taylor
> (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
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:
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).
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