Conda and Mamba
Both the miniconda3 and minforge modules include only conda, python, and a few other packages. Only the miniforge module provides mamba.
Mamba is a drop-in replacement of conda, and is faster at resolving dependencies than conda. For commands like conda install
and conda search
, conda
can be replaced with mamba
on Oscar. More details can be found in Mamba User Guide.
Conda Initialization
It is not recommended to initialize conda via conda init
.
Access Conda via Modules
To access the conda or mamba command, load either a miniconda3 or miniforge module and then run the source command
module load miniconda3/23.11.0s
source /oscar/runtime/software/external/miniconda3/23.11.0/etc/profile.d/conda.sh
shared among all users if the environment is installed in a shared directory
private to one user if the environment is installed in a user's private directory
The command 'conda info' shows important configurations for conda environment.
$ conda info
active environment : None
shell level : 0
user config file : /users/yliu385/.condarc
populated config files : /users/yliu385/.condarc
conda version : 23.1.0
conda-build version : not installed
python version : 3.10.9.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.34=0
__linux=5.14.0=0
__unix=0=0
base environment : /oscar/runtime/software/external/miniconda3/23.11.0 (writable)
conda av data dir : /oscar/runtime/software/external/miniconda3/23.11.0/etc/conda
conda av metadata url : None
channel URLs : 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
package cache : /oscar/runtime/software/external/miniconda3/23.11.0/pkgs
/users/yliu385/.conda/pkgs
envs directories : /oscar/runtime/software/external/miniconda3/23.11.0/envs
/users/yliu385/.conda/envs
platform : linux-64
user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.14.0-284.11.1.el9_2.x86_64 rhel/9.2 glibc/2.34
UID:GID : 140348764:2128288
netrc file : None
offline mode : False
Below are some important configurations:
envs directories
: a list of directories where a conda environment is installed by default. In the output of 'conda info' above, the first default directory to install a conda environment is a $HOME/anaconda.package cache
: a list of directories where downloaded packages are stored.
Create a New Conda Environment
To create a new conda environment in a default directory, run the following command:
conda create -n conda_environment_name
To create a new conda environment in a different directory, run the following command:
conda create -p /path/to/install/conda_environment_name
Activate a Conda Environment
After creating a conda environment, users can activate a conda environment to install or access packages in the environment via the following command.
conda activate conda_environment_name
If you need to activate a conda environment in a bash script, you need to source the conda.sh as shown in the following example bash script:
module load miniconda3/23.11.0s
source /oscar/runtime/software/external/miniconda3/23.11.0/etc/profile.d/conda.sh
conda activate my_env
Do NOT activate a conda environment before submitting a batch job if the batch job activates a conda environment. Otherwise, the batch job will not be able to activate the conda environment and hence fail.
To deactivate a conda environment, simply use the following command:
conda deactivate
Install Packages in an Active Conda Environment
To install a package, we need to first activate a conda environment, and then run
conda install package_name=version
The "=version" is optional. By default, conda install a package from the anaconda channel. To install a package from a different channel, run conda install
with the -c
option. For example, to install a package from the bioconda channel, run
conda install -c bioconda package_name
Delete a Conda Environment
To delete a conda environment, run
conda env remove -n conda_environment_name
Remove Caches
Conda may download lots of additional packages when installing a package. A user may use up all quota due to these downloaded packages. To remove the downloaded packges, run
conda clean --all
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