Miniconda Environments (Python)

DCAN Labs maintains lab-wide shared miniconda environments which are configured for ease of access to several of our commonly used Python tools such as Dcm2bids. Using the shared environment is in most cases preferred to individual users doing their own Python package installations and/or setting up environments in their MSI home directory.

IMPORTANT*: Environments and installed packages within the lab-wide environment must* have group read and write permissions open to ensure access for all group users! See here for info on using a umask to set your default permissions to be group-accessible. If you need to fix the permissions of an existing environment and/or package in the lab-wide environment, those can be found at /home/faird/shared/code/external/envs/miniconda3/mini3/envs/ and /home/faird/shared/code/external/envs/miniconda3/mini3/pkgs/ .

To load the DCAN labwide miniconda3 environment, first run the following command:
```
source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh
```
Note: It is advised to create your own environment within this miniconda3 for whatever you need miniconda3 for. That way we are not constantly changing the versioning of packages on the base environment.
To list the available environments within the miniconda environment:
```
conda info --envs
```
To activate a specific environment:
```
conda activate environment_name
```
To list the packages within an environment (if the environment is activated you do not need to specify the name):
```
conda list -n environment_name
```

To create a new conda environment, follow these instructions:

Load the miniconda3 base environment - as seen above
Check to make sure your environment does not already exist by running conda info --envs
Run conda create --name your_env_name
Run conda activate your_env_name
If you need to install with pip, run conda install pip
For installs on things included with miniconda3 run conda install package_name1 package_name2

Note: It is a list without commas. You can also install one by one.

More information about creating and using conda environments can be found here

You can also create an environment with a YAML file of requirements.

Load the miniconda3 base environment - as seen above
Check to make sure your environment does not already exist by using conda info --envs
Run conda env create -f /path/to/yaml/for/build.yml
Run conda activate the_env_name

Check out the conda user documentation and cheat sheet for further information.