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

[Barthelson, Roger A - (rogerab)]

Java is generally loaded as a module on TACC machines. It is possible that the java module on Lonestar or Stampede (wherever it runs) was updated and that the name change rendered the app inoperable. I have run into this sort of problem before with e.g. irods.

Roger
--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>


On June 26, 2014 at 11:38:53 AM, Dennis Roberts (dennis at iplantcollaborative.org<mailto: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<mailto: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<http://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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