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Creating a PBS/MPI cluster for bioinformatics – Part 3

Jun 21, 2012 in jenkins, bioinformatics | tutorial

This is the third and last part of this blog series. In this post we will install Structure (Pritchard Lab) and Torque PBS. We will configure a simple run in Structure using the two machines in our cluster.

Installing Structure

Installing structure is very simple. Download the latest version from Pritchard Lab page, decompress it and move the executables to a folder in your $PATH (or use symlinks). Here I’m using /usr/local/bin, but to keep things in order, I renamed the console folder (from structure_linux_console.tar.gz) to structure-console-2.3.3, because I like to know the tool and its version without having to browse it. Then I moved it under /opt/biouno, where I keep the executables used by the cluster. Finally, I created the symlink /usr/local/bin/structure that points to /opt/biouno/structure-console-2.3.3/structure.