On Wed, Sep 11, 2013 at 1:19 PM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:
Hi Peter
It's going to be one big machine, running both Galaxy server and the jobs. It's going to be a multi-process configuration. If that idea is terribly bad please let me know so I can give back the feedback.
It should be OK for a small number of users, but at some point if usage increases you will have to switch to a multi-machine setup (or just a single even bigger machine). If you do have access to a cluster, you can choose which tools are run locally and which are run on the cluster. Don't forget to budget for enough disk storage as well - Galaxy usage tends to generate a lot of intermediate files which your users may not routinely delete from their histories.
De novo assembly can also be for the human/mouse genome.
You may not have enough RAM, however I have no personal experience doing de novo assemblies of mouse/human to guide you here. Someone else on the list should be able to help, or since this is a general question try searching online, e.g. at seqanswers.com I'm not sure how easy it would be to setup your Galaxy to only allow one de novo assembly at a time - which would seem a sensible precaution given you may have multiple users (or the same user) trying to run assemblies in parallel. Peter