On Mon, Apr 29, 2013 at 3:38 PM, Ganote, Carrie L <cgan...@iu.edu> wrote:
> Hi Peter,
>
>>I'm not 100% sure but I think the  BLAST 2.2.26+ which Galaxy installed
>>via the Tool Shed will take priority over the system installed BLAST 2.2.28+
>>already on the cluster.
>
> Blast 2.2.26 probably would take priority, if I installed it =D but I didn't
> set up the missing tool dependencies for this reason.
>
>>(I am intending to update this as BLAST 2.2.26+ is quite old, but I am
>>currently struggling with the Galaxy unit test framework.)
>
> Anything that can be helped with? From my testing, 2.2.28 works fine
> with the tool repository 1f546099212f.

There's a regression with makeblastdb and the -parse_seqids option,
but otherwise BLAST 2.2.28+ fixes a lot of niggles I had with BLAST+.
http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html

On the Galaxy side there are still limitations in the test framework,
for example I'm stuck at the moment writing tests for makeblastdb:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014302.html

I may compromise and update the Tool Shed to use BLAST 2.2.27+
in the short term. That should just require regenerating all the test
output as things like e-values fluctuate between minor releases.

>>My guess is that your BLAST databases were updated around the same
>>time (or maybe one cluster node had a bad database copy or something).
>>But it could be down to the tool binaries themselves. Strange.
>
> It wouldn't be the first time our blast databases were uploaded with
> error, so that is quite possible.
>
>>Have you checked the data.py and binary.py files do include the
>>two classes GenericAsn1 and GenericAsn1Binary? It could be
>>an hg merge went wrong and your local copy of Galaxy is missing
>>them.
>
> That was it. I'm not sure why those weren't merged, but I went ahead
> and made those changes!

Oh good - nothing me or Nicola can be blamed for ;)

Thanks for the update,

Peter
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