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From "Donal K. Fellows" <donal.k.fell...@manchester.ac.uk>
Subject Re: Taverna Tool service
Date Tue, 08 Dec 2015 11:31:24 GMT
On 07/12/2015 19:25, Daniele Tartarini wrote:
> I would like to use Taverna server installed on an application server to
> run a workflow made of a Taverna Tool Service.
> It needs to run some bash commands on a remote HPC machine using SSH.
> The issue is that the HPC machine accepts only SSH connections via
> public key but not login/passwd.
> Is there any way to do it?

This seems like a reasonable request, and I really approve of how the 
HPC system is configured. But...

I'm not properly online now because of network problems, so I can't 
check against the Apache Taverna code, but if this part of the Tool 
Service is like it is in the parts of the Taverna 2 codebase that I've 
got available to me, you can't do it (easily). The problem is that the 
tool service *explicitly* stubs out the addition of key files; it looks 
like something that someone wanted to add but never got around to. :-(

So a workaround is required. You need to call the system ssh binary 
explicitly in your script with the -i option naming an identity file to 
load the private key from. That private key *needs* to be password-free 
as explicitly asking you for the unlock password will definitely fail — 
you might need to make a new keypair for this — and you should to upload 
the private key as part of the job initialisation before setting it 
operating. This isn't great, as the seams will be rather visible to you 
as a workflow author, but it ought to work.


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