Bioinformatics: Difference between revisions

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See [[Available_software#List_of_globally-installed_modules|Available software]] for a list of bioinformatics applications on our systems.
See [[Available_software#List_of_globally-installed_modules|Available software]] for a list of bioinformatics applications on our systems.
You can sort on 'Type', where bioinformatics software is categorized as 'bio'.
You can sort on <i>Type</i>, where bioinformatics software is categorized as <i>bio</i>.


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Some bioinformatics software is available as [[Python]] packages, which do not appear on the above list.  
Some bioinformatics software is available as [[Python]] packages, which do not appear on the list mentioned above.  
See [[Available Python wheels]] for a list of Python "wheels" customized for Alliance clusters.
See [[Available Python wheels]] for a list of Python <i>wheels</i> customized for our clusters.


=Data= <!--T:9-->
=Data= <!--T:9-->


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Some genome databases are available on our clusters, in <code>/cvmfs/ref.mugqic/genomes</code>.
Some genome databases are available on our clusters, provided by [https://genpipes.readthedocs.io/en/latest/c3gres/cvmfs_genomes.html MUGQIC].
Examine that directory and its subdirectories, e.g. with


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{{Command|ls /cvmfs/ref.mugqic/genomes}}
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or
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{{Command|ls /cvmfs/ref.mugqic/genomes/species}}
=Container Repository= <!--T:16-->
The Bioinformatics National Team maintains a repository of Apptainer (formerly Singularity) containers which provide common workflows and those workflows requiring preservation.  Learn more at [[Biorepo Containers]].


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Latest revision as of 18:49, 27 June 2023


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.



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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.

Some bioinformatics software is available as Python packages, which do not appear on the list mentioned above. See Available Python wheels for a list of Python wheels customized for our clusters.

Data

Some genome databases are available on our clusters, provided by MUGQIC.