In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...

This is the setting for bwa_wrapper in my universe_wsgi.ini:

bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

and this is what the job admin page shows:

It's in a different queue and does not use the smp setting I ask for...(It's the default setting)

any ideas?

7X26 minutes agotoolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3runningpython /mnt/ngs/analysis/svcgalaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="4" --fileSource=indexed --ref="/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta" --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=falsedrmaa://-V -q all.q -pe smp 1/4440144
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