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,
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).