> Where do I find info if the installed applications make use of multiple nodes 
> via MPI(etc) which would indicate the benefit of starting up X number of 
> nodes for faster processing?

You'll need to look at the individual tool documentation. In general, many 
tools uses multiple cores, few use MPI for multi-node computing.

> If a workflow has multiple initial inputs for say processing NGS exome data 
> from tumor and blood(gets compared later in the workflow) will each step get 
> sent to a different node(without a dependency) or will the entire workflow 
> run on one node?

If you've set up Galaxy to use a job scheduler (e.g. SGE/PBS), multiple nodes 
can be used. Multiple nodes will be used on the cloud:


> If I have NGS data for 20 patients sitting in a S3 bucket and want a specific 
> workflow run against each patient data input(s) does this require manual 
> selection of files by a user or can the workflow be automated?

Automation via the API is possible; unfortunately, most API documentation is in 
the Py/Sphinx docs for now, so you'll have to dig and/or use the sample scripts 
in <galaxy_dir>/scripts/api

> Can I programmatically start a workflow remotely(via REST) where I have 
> automated the process of uploading NGS data to S3 and know the input file(s) 
> per workflow?


> Is it possible to present credentials in a workflow for downloading a file 
> via S3 where I require authentication before a file can be downloaded?

You can restrict dataset access using role-based security.

> Does a roadmap exist for what is planned in the future?

Roadmap at a very high level is in this presentation: 

> For example any additional tools NGS tools like Abyss going to make into the 
> build?

The framework is being separated from tools. The best place to look for tools 
is in the toolshed, where there is an abyss wrapper:


> Interested in NGS software that handles the dynamics of cancer for gene 
> fusion events, CNVs(etc) when dealing with NGS data.

There is active work on cancer tools for Galaxy. Keeping an eye on the toolshed 
is a good idea here.


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