On Oct 17, 2012, at 3:53 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:

On Mon, Oct 15, 2012 at 11:49 AM, Liisa Koski <liisa.koski@basf.com> wrote:

...

Hello, I've installed a tool to my local Galaxy installation via my local ToolShed. I would like to run this tool locally, and not have it submitted to the grid.

I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners] section.

The tool id directly from the tool.xml file and the id from the shed_tool_conf.xml (same id found in the integrated_tool_panel.xml)

tool = local:/// galaxy.server:9009/repos/user/tool/1.0 = local:///

My job still gets submitted to the grid.

Hi,

I would also like to specify a tool_runner for a tool installed from the shed_tool. As Liisa, I can not find the correct tool id to use.

Any help? Thanks, Carlos

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

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

On Fri, Oct 19, 2012 at 12:00 AM, Fields, Christopher J <cjfields@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. chris