Installation[edit | edit source]

$ wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
$ bash Anaconda3*sh

Do you wish the installer to initialize Anaconda3
in your /gpfs/home/lleung/.bashrc ? [yes|no]
[no] >>> yes

Once installed, you will need to initialize and set up conda for your shell.

$ conda init zsh

## Restart or exec your shell
$ exec zsh

## If loaded properly, your shell should have a prefix of the environment name. Defaults to 'base'
(base) $

Usage[edit | edit source]

Command Description
conda create -n env_name pip python=version env_name is the name of the new environment. Packages follow.
conda env [-n] list Lists environments. -n lists deactivated environments.
conda list Environment currently activated
conda info –envs View list of packages installed on certain environment:
conda list -n env_name package_name See if a certain package is installed.
conda activate env_name Activates an environment
conda deactivate Exit from an environment
conda env remove -n env_name Removes an environment

Tasks[edit | edit source]

Setup an R environment[edit | edit source]

To create and install a particular package in a new environment, such as R:

$ conda create -n mro_env r-essentials
$ conda activate mro_env

To deactivate, run:

(base) $ conda deactivate

Setup R Bioconda[edit | edit source]

To get Bioconda working, you will need to add the following channels first:

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge

Once that is done, you can then install packages such as:

$ conda install r-metaboanalyst

Missing channels will result in a conflict and an empty UnsatisfiableError failure:

(rlang) ~ % conda create -n rmetabo -c bioconda r-metaboanalyst
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError:

After installing a package, it does not load and results in the following error:

‘GenomeInfoDbData’ was installed before R 4.0.0: please re-install it

This occurred only on the account with an old version of Miniconda and was fixed by installing the latest version of Anaconda and re-running all the commands above to reinstall the package.

See Also[edit | edit source]