Great solution...Glad I could help!On Dec 05, 2012, at 02:56 PM, Nate Coraor wrote:On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote: > I confirmed that you have to include the version numbers for these toolshed tools: > > This works: > toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrap
On Wed, Dec 5, 2012 at 10:56 PM, Nate Coraor wrote:
>
> Hi Thon,
>
> I just committed a fix for this in 75a97c971d36 that will be available in
> our next distribution release. It will also match from most to least
> specific so you can define all of:
>
> toolshed.g2.bx.psu.edu/repos/devteam/bwa_w
On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote:
> I confirmed that you have to include the version numbers for these toolshed
> tools:
>
> This works:
> toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 =
> drmaa://-V -q long.q -pe smp 4/
>
> this does not:
> toolshed.g2.
I confirmed that you have to include the version numbers for these toolshed tools:This works:toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 = drmaa://-V -q long.q -pe smp 4/this does not:toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper = drmaa://-V -q long.q -pe sm
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
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 t
