Goals: Demonstrate using conda to install a command-line application.

General Process

[]$ cd /project/<project-name>/<username>/
[]$ mkdir software
[]$ cd software
[]$ pwd
/project/<project-name>/<username>/software

[]$ module purge
[]$ module load miniconda3/24.3.0
[]$ conda create -p slim_env_4.2.2
...
## Package Plan ##
  environment location: /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2
...
# To activate this environment, use
#     $ conda activate /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2

Notice we haven’t performed any activate or install steps.

What do we notice about the installation location?

Create SLiM Environment

conda create -p ...

Using the -p option will create the environment in your current working folder.

[]$ conda install --help
...
  -p PATH, --prefix PATH
                        Full path to environment location (i.e. prefix).

[]$ cat ~/.conda/environments.txt
/home/<username>/.conda/envs/py_env
/project/<project-name>/<username>/conda/envs/r_env
/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2

Use / Activate this Environment

[]$ conda activate slim_env_4.2.2
EnvironmentNameNotFound: Could not find conda environment: slim_env_4.2.2
You can list all discoverable environments with `conda info --envs`.

[]$ conda info --envs
# conda environments:
#
base                     /apps/u/opt/linux/miniconda3/24.3.0
                         /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2
py_env                   /home/<username>/.conda/envs/py_env
r_env                    /project/<project-name>/<username>/conda/envs/r_env

This environment has no name and thus you must use the full path to activate.

[]$ conda activate /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2
(/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2) []$

Calling the SLiM command-line

The slim command is only available from within your activated conda environment.

As soon as you deactivate it, the command is no longer available.

(/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2) []$ conda install slim
(/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2) []$ slim --version
SLiM version 4.2.2, built May  5 2024 12:39:53
Git commit SHA-1: unknown (built from a non-Git source archive)

(/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2) []$ which slim
/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2/bin/slim

(/cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2) []$ conda deactivate

[]$ slim --version
bash: slim: command not found...

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ARCC Wiki

Example 03: Applications: SLiM

General Process

Create SLiM Environment

Use / Activate this Environment

Calling the SLiM command-line

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