The tool to fetch data isn't being run on your submit node but instead on
the cluster, which is the problem.

It's a fairly easy to solve problem:

   - In your job_conf you'll need to define a way to run jobs locally
   (either via local runner, or via a special queue dedicated to your submit
   node)
   - Then you'll need to specify that the upload tool is forced to that job
   runner.

Something like this (untested, probably invalid xml... )

<plugins workers="4">
  <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" />
  <!-- your torque runner here -->
</plugins>
<destinations default="cluster">
  <destination id="local" runner="local">
  <!-- your cluster dest here -->
</destinations>
<tools>

  <!-- we force the upload tool to the local job runner, thereby bypassing
the issue of internet access on the cluster nodes -->
  <tool id="upload1" destination="local" />
</tools>

Cheers,
Eric

2015-01-22 13:51 GMT-06:00 Fernandez Edgar <edgar.fernan...@umontreal.ca>:

>  Hello gents,
>
>
>
> I started this new thread because I have a showstopper for my installation
> of galaxy.
>
> Here’s my situation:
>
> 1.       I have a galaxy server that has internet access.
>
> 2.       My galaxy server is also my torque server and my only torque
> submit node.
>
> 3.       I have three torque compute nodes that DOESN’T have internet
> access.
>
>
>
> Now, I’ve tried uploading a file (larger than 2Gb) via and URL and it
> *fails*.
>
> However, I’ve added my galaxy server as a compute node and re-tried to
> upload the same file and I made sure the job will run on that machine and
> it *works*.
>
>
>
> Now, my compute nodes are in a network that is completely protected from
> the outside world.
>
> So no internet access.
>
>
>
> What are my option in this case?
>
>
>
> Cordialement / Regards,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
> *Université de Montréal*
>
> PAVILLON ROGER-GAUDRY, bureau X-218
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>



-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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