Hi, Thon I'm guessing here: but now that bwa is kept in the toolshed, the tool name appears to be toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride the default rather thant "bwa_wrapper" ?
This might be an unforseen consequence of the way the toolshed adapts tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags? On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer <thondeb...@me.com> wrote: > Hi, > > 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 ago > toolshed.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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