Which software is installed on Stallo

To find out what software packages are available, type:

module avail

Changes in application software

News about planned/unplanned downtime, changes in hardware, and important changes in software will be published on the HPC UiT twitter account https://twitter.com/hpc_uit and on the login screen of stallo. For more information on the different situations see news.

The easiest way to check which software and versions available is to use the module command. List all software available:

module avail

List all version of a specific software:

module avail software-name

Missing or new software

If there is any software missing on this list that you would like to have installed on Stallo, or you need help to install your own software, please feel free to contact the support personal about this: support@metacenter.no.

If there is software missing on Stallo that you would like to have, there are different options to install it: * Use our installation framework EasyBuild * Use a package manager like Conda or especially for bioinformatic software Bioconda * Compile it yourself and install into your home directory * Ask us to install for you

In this document we will show some ways of installing a new software. If you run into problems, need help or have question, please feel free to contact the support personal about this: support@metacenter.no.

Installing new software using EasyBuild

Our building and installation framework, EasyBuild can be used by you to install software into your own home directory. This is especially interesting for you if you need a software but it is probably not used by other users of Stallo, so a systemwide installation doesn’t make much sense.

To see if your software is available via the EasyBuild system have a look into the easyconfig github repository. if you can find a version of your software there.

Let’s assume you want to install the genome aligner Kraken2. We find a easyconfig file with the name Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb in the easyconfig repository.

Before we start the installation process we first have to load the necessary modules:

ml purge
ml EasyBuild

Before we actually build we can check the building process by adding –dry-run-short or -D to the build command:

eb Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb --dry-run-short

As you probably see, a long list of packages is printed with some packages being marked as missing. To automatically install all necessary dependencies we can add –robot and then run the installation:

eb Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb --robot

Before we can load your newly installed module, we have to add the path to the Lmod search path. You might have to do this from time to time, or even every time you use your software, as your local cache is regularly updated.

ml use ~/.local/easybuild/modules/all
ml Kraken2/2.0.7

Conda/ Bioconda

Many software packages, especially if they are python based, can be easily installed using the Conda package manager. For many bioinformatics software, Bioconda has become a nice solution.

A small tutorial can be found in the Python section of this documentation.