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

[Cathy Gresham]

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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