[blancha]

From the software point of view, the biggest question will be whether you want to install a queuing system, with TORQUE and Moab for example.

As GenoMax has pointed out, cluster administration is not trivial, and the biggest expense may be the salary of the personnel to administrate the cluster.

I really think off-site computing or cloud computing is the ideal solution for next-generation sequencing analysis. The administration of the cluster is then no longer your responsibility.

It may not always be possible however to do this at a reasonable cost. In Canada, researchers are provided access to computing clusters at no cost. I'm not sure how this could be done in other countries. For example, I wonder if it it cost feasible to use only Amazon Web Services. Perhaps not.

[GenoMax]

@blancha: @cmccabe works in a hospital so local security policy/HIPAA restrictions would most likely restrict/nix use of any external cloud based resources (unless the companies are willing to enter into business agreements).

@cmccabe does seem to have access to central IT but as you and I have pointed out this would add workload to their plate and would require them to acquire cluster admin expertise. It will depend on how good a salesperson @cmccabe is when talking with them.

For reference this question has now been posted on Biostars: https://www.biostars.org/p/167118/