On the new cluster (2021) environment modules are used to allow multiple versions of pieces of software to be installed “side-by-side” and to make software installation cleaner.

To get a list of installed software, issue on of these commands:

module avail
ml avail

Operating System: Ubuntu 16.04 LTS

• Installed on the nodes using PXE and preseeding.
• “Hands-free” install for a new node.

Cluster Resource Management

• SLURM
• Simple Linux Utility for Resource Management
  • From Lawrence Livermore National Laboratory
• https://slurm.schedmd.com/
• Version 15.08.7

Software Available on the Cluster

This is an incomplete list. Look in /usr/local and /usr/local/bin for specific programs. Feel free to ask the system administrators about software you can't see.

In general, and where possible, we recommend that you install the software you want in your own home directory. This gives you complete control over the versions of software and associated packages that you are using. You can use conda to manage specific software versions within different environments, or use Singularity to manage your software within a container. These are described on separate pages within these notes.

If you need a later version of these tools, first look at installing the version you want yourself either directly in your home directory or using conda. If that is not possible, or if you have difficulty installing the software you need, please contact one of the system administrators.

• R currently 3.5.1
• Python 2.7.12 and Python 3.5.2
  • Use python3 to run python 3.5.2
  • Use conda to install a specific version of python for yourself.
• ABYSS
• agalma
• augustus
• bedtools
• blast
• bowtie
• bowtie2
• bwa
• cufflinks
• eigenstrat
• falcon
• fastqc
• hmmer
• HYPHYMP
• jgil
• matlab
• merlin
• mothur
• plink
• samtools
• SAS
• tophat
• vcftools