On Wed, Apr 24, 2013 at 11:40 PM, Ganote, Carrie L <cgan...@iu.edu> wrote:
> Hi list,
> I have a newly installed Galaxy instance (security_2013.04.08) and I am
> testing out NCBI Blast+ on it. I'm having trouble getting it to run.
> I'm using the following tools from the Galaxy Main Toolshed:
> blast_datatypes b3a3ba0c1d47
> ncbi_blast_plus 1f546099212f

Those are the latest releases on the main ToolShed, which is good.

Revision: 5:b3a3ba0c1d47
Version 0.0.15

Revision: 8:1f546099212f
Version 0.0.17

How did you install them? Via the automated Tool Shed install,
or manually?

How did you setup the databases?

> Looks like blast is being called fine, but I get this:
> Fatal error: Matched on Error:
> Error: NCBI C++ Exception:
> "/N/soft/rhel6/ncbi-blast+/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp",
> line 925: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to
> access NULL pointer.

Searching for that error suggests it can be triggered by a bad database:

If this is an NCBI database, check the MD5 checksums and/or
redownload it.

If this is your own database, try deleting it and rebuilding it from
the FASTA file.

> WARNING:galaxy.datatypes.registry:Error loading datatype with extension
> 'asn1': 'module' object has no attribute 'GenericAsn1'
> WARNING:galaxy.datatypes.registry:Error loading datatype with extension
> 'asn1-binary': 'module' object has no attribute 'GenericAsn1Binary'
> Anyone seen this?

I think this might be a fault in Galaxy with some recently added
ASN1 formats (which we will later be subclassing for using
with BLAST or other NCBI tools). The commit was here:



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