Bioinformatics

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

External support

The Canadian Centre for Computational Genomics (C3G), is a bioinformatics core facility affiliated with McGill University. It collaborates with the Alliance to offer bespoke bioinformatics services and supports the bioinformatics community as members of the Alliance's Bioinformatics National Team. C3G maintains two CVMFS repositories:

• soft.mugqic contains many open-source bioinformatics tools installed as modules
• ref.mugqic contains reference genomes and their indices and annotations for many common model organisms.

For requests or questions about mugqic repositories, contact C3G at [1] or via their website computationalgenomics.ca.

Software

See Available software for a list of bioinformatics applications on our systems. You can sort on Type, where bioinformatics software is categorized as bio.

Much bioinformatics software is available as Python packages. Python packages which have been customized for use on our systems are listed at Available Python wheels. Packages not found there may be obtained from the internet in the usual fashion. See Python for guidance on both these things.

Data

Some bioinformatics databases are available on our clusters. Look in the following locations:

• /cvmfs/ref.mugqic (supported by C3G, see above)
• /cvmfs/bio.data.computecanada.ca
• /cvmfs/datahub.genap.ca
• /cvmfs/ref.galaxy
• /cvmfs/public.data.computecanada.ca
• /datashare (Graham Reference Dataset Repository, external documentation)

Not all of these are available on all clusters, and they are not uniformly supported.