Hi Ross,

I was indeed expecting something like that and when I tried what you suggestyed, it worked :)
you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set in the universe_wsgi.ini...

So indeed the toolshed move of BWA breaks the individual tool_runner settings and makes for one ugly config file now...
But at least we found a workaround...



On Dec 05, 2012, at 01:52 PM, Ross <ross.laza...@gmail.com> wrote:

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:

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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