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


General Process

[salexan5@mblog1 ~]$ cd /project/arcc/salexan5/
[salexan5@mblog1 salexan5]$ mkdir software
[salexan5@mblog1 salexan5]$ cd software
[salexan5@mblog1 software]$ pwd
/project/arcc/salexan5/software

[salexan5@mblog1 software]$ conda create -p slim_env_4.2.2
...
## Package Plan ##
  environment location: /cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2
...
# To activate this environment, use
#     $ conda activate /cluster/medbow/project/arcc/salexan5/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.

[salexan5@mblog2 ~]$ conda install --help
...
  -p PATH, --prefix PATH
                        Full path to environment location (i.e. prefix).

[salexan5@mblog2 ~]$ cat ~/.conda/environments.txt
/home/salexan5/.conda/envs/py_env
/project/arcc/salexan5/conda/envs/r_env
/cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2

Use / Activate this Environment

[salexan5@mblog2 ~]$ 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`.
[salexan5@mblog2 ~]$ conda info --envs
# conda environments:
#
base                     /apps/u/opt/linux/miniconda3/24.3.0
                         /cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2
py_env                   /home/salexan5/.conda/envs/py_env
r_env                    /project/arcc/salexan5/conda/envs/r_env

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

[salexan5@mblog2 ~]$ conda activate /cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2
(/cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2) [salexan5@mblog2 ~]$

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/arcc/salexan5/software/slim_env_4.2.2) [salexan5@mblog2 ~]$ conda install slim
(/cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2) [salexan5@mblog2 ~]$ 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/arcc/salexan5/software/slim_env_4.2.2) [salexan5@mblog2 ~]$ which slim
/cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2/bin/slim

(/cluster/medbow/project/arcc/salexan5/software/slim_env_4.2.2) [salexan5@mblog2 ~]$ conda deactivate

[salexan5@mblog2 ~]$ slim --version
bash: slim: command not found...

 

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