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.

http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Revision: 5:b3a3ba0c1d47
Version 0.0.15

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962

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:

https://bitbucket.org/galaxy/galaxy-central/commits/d6f866cbf12d0242089fbbbfb799fb20600441cf
https://bitbucket.org/galaxy/galaxy-dist/commits/d6f866cbf12d0242089fbbbfb799fb20600441cf

Curious,

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to