Sequencing analysis server

Question

[munnadt2]

Hello All

I am trying to set up a computing server in our laboratory, and need your suggestions in setting up the optimized platform.

Requirements/Intended uses of the server: RNA-Sequencing analysis (Mapping, alignment and the downstream analysis), Bio-Linux, Cytoscape, Local installation of Galaxy, Storage of RNA-Seq data.

We usually work on Macs, and I have a high-end PC running Ubuntu Linux that I intend to make into a server.

I request your inputs on:

1. Is it possible to write scripts on the mac, and run them on the server batch-wise or individually? If so, how (any links would be welcome)?
2. What could be the best server to access from a Mac- would Ubuntu server work fine, or do I need Mac server or Windows server? (They are in the same network)

Thank You.

Best M

Answer 1

[DG]

You can access a Linux server on a network just as easily from a Mac running OSX as you can another Linux machine or a Windows machine. There is no difference from a practical end user perspective other than what you use to do it. For this kind of work you are going to be likely doing 90% of the analysis from the command line anyway. So it is as simple as opening terminal and using SSH to log in to the server.

Same goes for writing scripts and running them on the server. Most of the time where you write them and where you run them doesn't matter 9Windows is a bit of an outlier if you are talking about writing scripts that you need to be cross-platform). OS X is UNIX under the hood so there are typically no issues (or not many) with file formats and the like. How you transfer files, scripts, and data back and forth is a matter of personal preference. I use FTP for large data transfers but I also have Dropbox installed on my Macbook and on my Linux workstation that keeps my Dropbox files in sync. I also use GitHub for development work and keeping the repositories synced between machines.

[mcc]

I do a very similar thing with my network.