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

[Dennis Roberts]

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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