Bioconda: Difference between revisions
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(Created page with "= General = * Home page: https://bioconda.github.io/index.html * List of available packages: https://bioconda.github.io/conda-package_index.html = Links = ARC Software pages") |
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* List of available packages: https://bioconda.github.io/conda-package_index.html | * List of available packages: https://bioconda.github.io/conda-package_index.html | ||
= Bioconda on ARC = | |||
== Available modules == | |||
To activate | |||
<pre> | |||
$ module avail bioconda | |||
-------------------- /global/software/Modules/4.6.0/modulefiles ----------------- | |||
bioconda/2018.11 bioconda/conda3 | |||
$ module load biconda/2018.11 | |||
Loading bioconda/2018.11 | |||
Loading requirement: bioconda/conda3 | |||
</pre> | |||
Check software | |||
<pre> | |||
$ samtools --version | |||
samtools 1.9 | |||
Using htslib 1.9 | |||
Copyright (C) 2018 Genome Research Ltd. | |||
$ salmon --version | |||
salmon 0.11.3 | |||
$ kraken --version | |||
Kraken version 0.10.6-unreleased | |||
Copyright 2013-2015, Derrick Wood (dwood@cs.jhu.edu) | |||
</pre> | |||
Get the list of installed packages: | |||
<pre> | |||
$ conda list | |||
.... | |||
.... | |||
</pre> | |||
= Links = | = Links = | ||
[[ARC Software pages]] | [[ARC Software pages]] | ||
Latest revision as of 16:31, 21 March 2024
General
- Home page: https://bioconda.github.io/index.html
- List of available packages: https://bioconda.github.io/conda-package_index.html
Bioconda on ARC
Available modules
To activate
$ module avail bioconda -------------------- /global/software/Modules/4.6.0/modulefiles ----------------- bioconda/2018.11 bioconda/conda3 $ module load biconda/2018.11 Loading bioconda/2018.11 Loading requirement: bioconda/conda3
Check software
$ samtools --version samtools 1.9 Using htslib 1.9 Copyright (C) 2018 Genome Research Ltd. $ salmon --version salmon 0.11.3 $ kraken --version Kraken version 0.10.6-unreleased Copyright 2013-2015, Derrick Wood (dwood@cs.jhu.edu)
Get the list of installed packages:
$ conda list .... ....