Hi,
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:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/samtools/1.2/iuc/package_samtools_1_2/f6ae3ba3f3c1/env.sh; MEM=`expr "${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, Nikolaos