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 tool_script.sh file is generated automatically by Galaxy
or still user can add something there? If it generates automatically then
is this a bug?

cat tool_script.sh:


# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
   exit 42
export PACKAGE_BASE; .
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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