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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