On Mon, Apr 29, 2013 at 2:53 PM, Ganote, Carrie L <cgan...@iu.edu> wrote:
>
> Hi Peter,
>
> >How did you install them? Via the automated Tool Shed install,
> >or manually?
>
> I installed the tool wrappers via the Tool Shed, and Blast 2.2.28 is
> already installed on my cluster so I put the path in my environment setup
> file.

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.

(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.)

> >How did you setup the databases?
>
> I added the existing databases to my .loc files. They all show up in the
> menu for Blast so I think that checks out. Sometimes I've noticed that emacs
> has a problem with adding tabs so I used pico. Our HPC team updates the
> blast databases monthly, but we run with them from the bare iron to so I
> don't think they're the culprits.

I still use emacs for tabs, but curse regularly when I accidentally do
Apple+Q and quite the terminal (rather than Ctrl+Q, tab).

> >>
> >> "/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.
>
> We were getting the null pointer exception even from the command line when
> we ran it with more than one thread. Funny, we reinstalled Blast 2.2.28 and
> this error went away. Who knows?

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.

> >> 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'
>
> >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
>
> Nothing in those commits looks alarming, so I'm not sure where the bug is.
> Now blast works, but I'm still getting this error with every tool I run. I
> think I'll undo the commits for now.
>
> Thanks!
>
> Carrie Ganote

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.

Peter
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