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

[Ghiban, Cornel]

Adding this should work (at least on lonestar):

load java64/1.7.0

Cornel

On Thu, 2014-06-26 at 13:58 -0500, Cathy Gresham wrote:
>  
> Do not know if this helps but one of the out files from the failed job
> lists the env settings that you set up for
> interproscan:
>  
> OUT TEXT FILE:
> # Environmental settings for interproscan-5.44.0u1:
> module purge
> module load TACC
> module swap intel gcc
> module load iRODS
> module load perl
> module load launcher
> THREADS=1
> OWD=$PWD
>  
> # Unpack bin directory
> tar -zxf bin.tgz
> PATH=${PATH}:${OWD}/bin
> # Deployed in the TACC scratch projects space dedicated to iPlant
> # until we can develop a module for InterproScan
> IPRSCAN="/scratch/projects/tacc/iplant/interproscan/5/interproscan-5-44.0/"
> PATH=${PATH}:${IPRSCAN}:${IPRSCAN}/bin
> 
> 
> interproscan.sh which is throwing the java error has this code to
> identify java:
>  
> JAVA=$(type -p java)
>  
> if [[ "$JAVA" == "" ]]; then
>     printf 'Java not found. Please install java\n'
>     printf 'and place it on your path,\n'
>     printf 'or edit the interproscan.sh script to refer to your java
> installation.\n'.
>     exit 1
> fi
> VERSION=$("$JAVA" -Xms32M -Xmx32M -version 2>&1 | { read X; printf '%
> s' "${X#*\"}"; } )
> MAJOR_VERSION=${VERSION%%.*}
> MINOR_VERSION=${VERSION#*.}
> MINOR_VERSION=${MINOR_VERSION%%.*}
>  
> if [[ "${MAJOR_VERSION}" == "1" && "${MINOR_VERSION}" -lt "6" ]];
> then
>     printf 'Java version 1.6 or above required\n'
>     printf 'Detected version %s.%s\n' "${MAJOR_VERSION}"
> "${MINOR_VERSION}"
>     printf 'Install the correct version \n'
>     printf 'or edit the interproscan.sh script to disable version
> check.\n'
>     exit 1
> fi
>  
> "$JAVA" -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts
> -XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar
> interproscan-5.jar $@ -u $USER_DIR
>  
>  
> 
> >>> "Barthelson, Roger A - (rogerab)" <rogerab at email.arizona.edu>
> 6/26/2014 1:42 PM >>>
> 
> 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
> Web: www.iplantcollaborative.org/
> 
> On June 26, 2014 at 11:38:53 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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> > > Iplant-api-dev at iplantcollaborative.org
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> > 
> > 
> > _______________________________________________ 
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> > 
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