Bioconda
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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/2024-10
- BioConda/2024-10 is based on the
biocondaandconda-forgechannels.
- It does not depend nor use the Anaconda
baseandanacondachannels to avoid any licensing complications. - It was installed in October 2024 and includes a large number of more popular BioConda packages.
You can load the module
$ module load biconda/2024-10 ### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ### This is a stub module. It does not activate the central BioConda install. If you want to activate BioConda/2024-10 please use the following command in your job script: source /global/software/bioconda/init-2024-10 Module activation does not work propely for this BioConda due to technical limitaions. This may change in the future. ### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ### Loading bioconda/2024-10 ERROR: Module evaluation aborted
The message indicate that the module cannot activate BioConda correctly, so you have to use the command
source /global/software/bioconda/init-2024-10
instead.
Once you have BioConda activated you can check the software
$ samtools --version samtools 1.21 Using htslib 1.21 Copyright (C) 2024 Genome Research Ltd. $ salmon --version version : 0.8.1 $ kraken --version Kraken version 1.1.1 Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26@jhmi.edu)
Get the full list of installed packages:
$ conda list ....