Goal: What are channels and how can they be used and configured.

What are Channels?

Managing channels: Conda channels are the locations where packages are stored. They serve as the base for hosting and managing packages. Conda packages are downloaded from remote channels, which are URLs to directories containing conda packages.

Can’t find package?

Example: I’ve heard SLiM is available to install via conda?

[]$ conda search slim
Loading channels: done
No match found for: slim. Search: *slim*
# Name                       Version           Build  Channel
r-slim                         0.1.1   r36h6115d3f_0  pkgs/r
...
r-waveslim                     1.8.4   r43h640688f_0  pkgs/r

Additional Common Channels:

bioconda: (>10K packages) Bioconda is a distribution of bioinformatics software realized as a channel for the versatile Conda package manager.
conda-forge packages:

[]$ conda search bioconda::slim
Loading channels: done
No match found for: bioconda::slim. Search: bioconda::*slim*
# Name                       Version           Build  Channel
gargammel-slim                 1.1.2      h06294c5_5  bioconda
...
slimfastq                       2.04      he1b5a44_0  bioconda
...
slimm                          0.3.4      hf1761c0_4  bioconda

[]$ conda search conda-forge::slim
Loading channels: done
# Name                       Version           Build  Channel
slim                           3.3.2      he1b5a44_0  conda-forge
...
slim                           4.2.2      h59595ed_0  conda-forge

Add Channel

[]$ conda config --add channels conda-forge

[~]$ cat ~/.condarc
...
channels:
  - conda-forge
  - defaults
[]$ conda info

[]$ conda info
...
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
...

Search for SLiM

[]$ conda search slim
Loading channels: done
# Name                       Version           Build  Channel
slim                           3.3.2      he1b5a44_0  conda-forge
...
slim                           4.2.2      h59595ed_0  conda-forge

No need to explicitly define the channel in the search command as it is not part of our general conda configuration.

Channel Options

The channel option can be defined within a number of other commands, such as conda install:

[]$ conda install --help
usage: conda install [-h] [--revision REVISION] [-n ENVIRONMENT | -p PATH] [-c CHANNEL] [--use-local] [--override-channels] [--repodata-fn REPODATA_FNS]
                     [--experimental {jlap,lock}] [--no-lock] [--repodata-use-zst | --no-repodata-use-zst] [--strict-channel-priority] [--no-channel-priority]
                     [--no-deps | --only-deps] [--no-pin] [--copy] [--no-shortcuts] [--shortcuts-only SHORTCUTS_ONLY] [-C] [-k] [--offline] [--json] [-v] [-q] [-d]
                     [-y] [--download-only] [--show-channel-urls] [--file FILE] [--solver {classic,libmamba}] [--force-reinstall]
                     [--freeze-installed | --update-deps | -S | --update-all | --update-specs] [-m] [--clobber] [--dev]
                     [package_spec ...]
...
Channel Customization:
  -c CHANNEL, --channel CHANNEL
                        Additional channel to search for packages. These are URLs searched in the order they are given (including local directories using the
                        'file://' syntax or simply a path like '/home/conda/mychan' or '../mychan'). Then, the defaults or channels from .condarc are searched (unless
                        --override-channels is given). You can use 'defaults' to get the default packages for conda. You can also use any name and the .condarc
                        channel_alias value will be prepended. The default channel_alias is https://conda.anaconda.org/.
...

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Example 02: R and TidyVerse

Workshop Home

Intro to Using Conda

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Example 03: Applications: SLiM

ARCC Wiki

Conda Channels