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From alaninmcr <alanin...@googlemail.com>
Subject Re: External Tool Service and SSH
Date Mon, 24 Oct 2016 11:27:26 GMT
On 20/10/2016 12:25, Nina Wolfram wrote:
> Hi everyone,

Hello

For some reason, it seems to be using "tmp/" rather than "/tmp/" as the 
directory. Can you check the definition of the location you are running 
the tool on?

You can find that under File -> Preferences -> Tool invocation

> I recently started working with the Taverna Workbench 2.5. and want to
> create a workflow running an External Tool on a remote machine.
> Establishing the SSH connection works, but there seems to be an error
> when creating the temporary directory for the invocation. The taverna
> logfiles give me the following output:
> /
> /
> /INFO  2016-10-19 13:12:53,440
> (de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation:136)
> - Changing remote directory to tmp/

[snip]

> It seems there is one change of directory too much: in the filesystem I
> end up with a directory structure of /tmp/tmp/usecase-5420555556213764519.
> Is there any workaround for this? (Or am I maybe doing something wrong?)

I think the location is set incorrectly.

> I also have a follow-up question:
> Eventually I'd like to run this workflow using the Taverna Player /
> Taverna Player Portal on an installation of Taverna Server. How do I
> transmit the credentials for the SSH connection in that scenario?

I know how to do it on a Taverna Server instance using
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/security/credentials

I am not sure about the player.

> Thanks in advance for your help!
>
> Nina

Alan


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