On Oct 19, 2012, at 9:35 AM, Carlos Borroto <carlos.borr...@gmail.com> wrote:

> On Fri, Oct 19, 2012 at 12:00 AM, Fields, Christopher J
> <cjfie...@illinois.edu> wrote:
>> My local one is set up like this and it works (for augustus):
>>    toolshed.g2.bx.psu.edu/repos/bjoern-gruening/augustus/augustus/0.1 = 
>> pbs:///default/-l ncpus=1,mem=8gb,walltime=24:00:00/
>> The above is the path in within the shed repo.
>> chris
> Hi Chris,
> This was quite helpful, although I don't know what you mean by "path
> in within the shed repo".

Apologies, not enough caffeine.  But you seemed to work it out, so it all came 
together in the end :)

> The tool I was trying to specify a runner
> for is "ncbi_blastn_wrapper" form the "ncbi_blast_plus" repository.
> This is the past to the tool under the local "shed_tools" directory:
> shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/9d5beacae92b/ncbi_blast_plus/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
> I did however, now that I see what is the overall look of IDs in these
> cases, find a way to come up with the correct ID. I put a job to run
> and looked in "Admin/Manage jobs", the column "Tool" displays the
> correct ID of the tool running. In my case it ended being:
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.13
> Thanks a lot for giving me a good hint of what to look for!,
> Carlos

It would be nice to have a shorter alias for these, but maybe that's not 
possible at the moment.

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