Goals: Demonstrate using conda to install a command-line application.
...
General Process
| Code Block |
|---|
[]$ 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 |
| Info |
|---|
Notice we haven’t performed any activate or install steps. What do we notice about the installation location? |
...
Create SLiM Environment
| Code Block |
|---|
conda create -p ... |
| Info |
|---|
Using the -p option will create the environment in your current working folder. |
| Code Block |
|---|
[]$ conda install --help
...
-p PATH, --prefix PATH
Full path to environment location (i.e. prefix). |
| Code Block |
|---|
[]$ 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
| Code Block |
|---|
[]$ 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`. |
| Code Block |
|---|
[]$ 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 |
| Note |
|---|
This environment has no name and thus you must use the full path to activate. |
| Code Block |
|---|
[]$ 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
| Info |
|---|
The slim command is only available from within your activated conda environment. As soon as you deactivate it, the command is no longer available. |
| Code Block |
|---|
(/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... |
...