Tools & Applications

In addition to the usual selection of Linux and Bash utilities (tar, wget, rsync, htop, pigz, etc) the following applications are available system-wide:

In general though, and in order to keep the cluster lean and mean, we don’t system install applications (or libraries) as it’s easier for users to manage their own specific needs using tools like Bioconda and Singularity, however for cases where this isn’t possible we still aim to make certain applications available (usually under /mnt/shared/apps) where they’re visible to all nodes of the cluster.

Note

To run applications not located on the default path, you must provide the full path to the executable in question, eg /mnt/shared/apps/java/13.0.2/bin/java. This is usually the case when multiple versions exist.

Aspera

  • /mnt/shared/apps/aspera/3.9.2

  • On default path: yes

The Aspera client can be used to efficiently download very large data sets from remote clients (often sequencing centres).

Bioconda

  • $APPS/conda (once installed)

  • On default path: yes

Bioconda is a package manager that specializes in providing bioinformatics software. We have a custom install script to handle its installation for you which can be run using:

$ install-bioconda

Warning

In order to maintain compatibility with the system’s backup and data policies, you should not attempt to install Bioconda using any other method than the script listed above.

Databases

  • /mnt/shared/apps/databases

  • On default path: n/a

We maintain several popular bioinformatics Database Mirrors which are accessible over the high-performance storage network from any node in the cluster.

Java

  • /mnt/shared/apps/java

  • On default path: no

Updated versions of the Java JDK are available here. CentOS 8 ships with JDK 8 by default, although you can also get other versions via Bioconda.