makeblastdb wrapper
Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you
On Mon, Jul 16, 2012 at 6:10 PM, Espin, Almudena <a.p.almudena@cranfield.ac.uk> wrote:
Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you
I'm already trying to merge Edward Kirton's patches which implement this - I'm on holiday at the moment though. Peter P.S. My branch is here - not really finished yet: https://bitbucket.org/peterjc/galaxy-central/src/blastdb
On Mon, Jul 16, 2012 at 7:07 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 16, 2012 at 6:10 PM, Espin, Almudena <a.p.almudena@cranfield.ac.uk> wrote:
Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you
I'm already trying to merge Edward Kirton's patches which implement this - I'm on holiday at the moment though.
Peter
P.S. My branch is here - not really finished yet: https://bitbucket.org/peterjc/galaxy-central/src/blastdb
I moved those changes to a more recent branch with some other BLAST work, and updated my open pull request: https://bitbucket.org/peterjc/galaxy-central/src/blast_tweaks https://bitbucket.org/galaxy/galaxy-central/pull-request/48 Assuming no major problems that I've missed, this could be in the next Galaxy release. Peter
On Mon, Jul 16, 2012 at 7:07 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 16, 2012 at 6:10 PM, Espin, Almudena <a.p.almudena@cranfield.ac.uk> wrote:
Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you
I'm already trying to merge Edward Kirton's patches which implement this - I'm on holiday at the moment though.
Peter
P.S. My branch is here - not really finished yet: https://bitbucket.org/peterjc/galaxy-central/src/blastdb
Hi Almudena, It took longer than I expected (we had a server problem which delayed things), but support for local BLAST databases as a datatype in the history is working nicely for us now. I've uploaded the updated BLAST+ wrappers and datatype definitions to the ToolShed as v0.0.14, hopefully you or another brave person can test them next week. My thanks again to Edward for his earlier work for on this - very useful. Note that I haven't enabled the masking or taxon options yet (I haven't had time to test them). Regards, Peter
participants (2)
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Espin, Almudena -
Peter Cock