All Saba and Luna compute servers run CentOS 6 Linux. The /opt/common directory is mounted on all compute servers in the saba and luna clusters. It includes many Next-Gen Sequence Analysis packages, such as bwa, samtools and additional versions of python, biopython, R and BioConductor among others.

In an effort to keep track of frequently changing software versions, we are now using this path structure:

/opt/common/CentOS_6/package/version/

For example the latest bwa is at:

/opt/common/CentOS_6/bwa/bwa-0.7.12/bwa

R-3.2.0 is at:

/opt/common/CentOS_6/R/R-3.2.0/bin/R

You can set these paths in your .bashrc or use the full path in your code. If you put paths in your .bashrc make sure that you source it or somehow add the path to your grid engine scripts.

If you need additional software, check with us to see if we already have it installed. We can install packages for you globally or help you with your own install.