strange submit script

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strange submit script

Nikolaos Tur

Galaxy 16.04, sge as batch system.
There is strange submit script from one job which replicates whole Galaxy home directory to the working directory for jobs and does this 2 times.
Am I correct that file is generated automatically by Galaxy or still user can add something there? If it generates automatically then is this a bug?



# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
   exit 42
PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1/; MEM=`expr "${GALAXY_SLOTS:-16}" \* 48 - 16` ;  workdir=`pwd`; echo "workdir is $workdir"; cd $LOCAL; echo "Running Trinity from `pwd`";  Trinity --max_memory "${MEM}G" --CPU "${GALAXY_SLOTS:-16}" --bflyHeapSpaceMax "32G" --bflyHeapSpaceInit "2G" --bflyGCThreads "6"   --left /home/galaxy/database/files/000/dataset_81417.dat --right /home/galaxy/database/files/000/dataset_81418.dat --seqType fq --SS_lib_type RF --group_pairs_distance 500   > /home/galaxy/database/files/000/dataset_81515.dat 2>&1  || (ec=$? ; cp -pr . $workdir; cd $workdir; cat /home/galaxy/database/files/000/dataset_81515.dat >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit $ec);  cp -pr . $workdir; cd $workdir

Output is:
workdir is /home/galaxy/database/jobs_directory/000/51718/working
Running Trinity from /home/galaxy

It means that in "cd $LOCAL" LOCAL variable is undefined. And then there is a bunch of copies from home directory.

Thanx for the help,

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