Bioconda: Difference between revisions
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| Line 12: | Line 12: | ||
$ module avail bioconda | $ module avail bioconda | ||
-------------------- /global/software/Modules/4.6.0/modulefiles ----------------- | -------------------- /global/software/Modules/4.6.0/modulefiles ----------------- | ||
bioconda/ | bioconda/2024-10 | ||
</pre> | |||
* '''BioConda/2024-10''' is based on the <code>bioconda</code> and <code>conda-forge</code> channels. | |||
: It does not depend nor use the Anaconda <code>base</code> and <code>anaconda</code> channels 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 | |||
<pre> | |||
$ 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 | |||
Loading bioconda/ | ERROR: Module evaluation aborted | ||
</pre> | </pre> | ||
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 | |||
<pre> | <pre> | ||
$ samtools --version | $ samtools --version | ||
samtools 1. | samtools 1.21 | ||
Using htslib 1. | Using htslib 1.21 | ||
Copyright (C) | Copyright (C) 2024 Genome Research Ltd. | ||
$ salmon --version | $ salmon --version | ||
version : 0.8.1 | |||
$ kraken --version | $ kraken --version | ||
Kraken version | Kraken version 1.1.1 | ||
Copyright 2013- | Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26@jhmi.edu) | ||
</pre> | </pre> | ||
Get the list of installed packages: | Get the full list of installed packages: | ||
<pre> | <pre> | ||
$ conda list | $ conda list | ||
.... | .... | ||
</pre> | </pre> | ||
Revision as of 21:26, 14 November 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/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 ....