[Iplant-api-dev] Error with InterProScan via DE

[Nicole Hopkins]

I figured it wasn't a DE fix. I think we'll need assistance from folks at
TACC to help with this.


On Thu, Jun 26, 2014 at 11:38 AM, Dennis Roberts <
dennis at iplantcollaborative.org> wrote:

> Hi Nicole,
>
> It appears that the issue is that Java isn’t available in the location
> where the app is being executed. If this is the case then this isn’t
> something that can be fixed in the DE.
>
> Thanks,
> Dennis
>
> On Jun 26, 2014, at 11:30 AM, Nicole Hopkins <
> nicole at iplantcollaborative.org> wrote:
>
> Up until a few weeks ago, the InterProScan5-44.0 tool in the DE was
> working quite well. Fiona and Cathy have been using it, and have recently
> had jobs complete, but with empty datasets returned.
> A look at the .out log from the tool gives this error message:
>
>  TACC Launcher -> Iniating task 1 on c339-104.ls4.tacc.utexas.edu (time
> /scratch/projects/tacc/iplant/interproscan/5/interproscan-5-44.0/interproscan.sh
> --formats tsv,gff3,xml --iprlookup --goterms --pathways --tempdir /tmp
> --output-dir output --input split_fasta/seqfile.0 )
> Java not found. Please install java
> and place it on your path,
> or edit the interproscan.sh script to refer to your java installation.
> .TACC: Shutting down parallel environment.
> TACC: Shutdown complete. Exiting.
>
> {"status":"success","message":"","result":{"id":54209,"name":"InterproScan5-44.0_example_test2-2014-06-26-16-50-
>
> This is running via on v1 of the API. I am assuming it will be running via
> Agave as well, but is there a fix that can be put in place near term?
>
>
> --
> Nicole Hopkins
> Scientific Initiatives Coordinator
> iPlant Collaborative- University of Arizona
> (520) 626-7390
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>
>


-- 
Nicole Hopkins
Scientific Initiatives Coordinator
iPlant Collaborative- University of Arizona
(520) 626-7390
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