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Goals: Demonstrate using conda to install a command-line application.
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General Process
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[]$ 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
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## Package Plan ##
environment location: /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2
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# To activate this environment, use
# $ conda activate /cluster/medbow/project/<project-name>/<username>/software/slim_env_4.2.2 |
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Notice we haven’t performed any activate or install steps. What do we notice about the installation location? |
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Create SLiM Environment
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conda create -p ... |
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Using the |
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[]$ conda install --help
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-p PATH, --prefix PATH
Full path to environment location (i.e. prefix). |
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[]$ 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 |
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Use / Activate this Environment
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[]$ 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`. |
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[]$ 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 |
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This environment has no |
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[]$ 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) []$ |
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Calling the SLiM command-line
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The As soon as you deactivate it, the command is no longer available. |
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(/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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