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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| #!/bin/bash | ||
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| # Source .bashrc to load aliases | ||
| if [ -f ~/.bashrc ]; then | ||
| source ~/.bashrc | ||
| fi | ||
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| # Print the aliases | ||
| echo "Alias List with Descriptions:" | ||
| echo "" | ||
| echo "1. rmge ='micromamba activate rmg_env'" | ||
| echo " - Activates the 'rmg_env' environment using Conda." | ||
| echo "" | ||
| echo "2. arce ='micromamba activate arc_env'" | ||
| echo " - Activates the 'arc_env' environment using Conda." | ||
| echo "" | ||
| echo "3. rmg ='python-jl /home/rmguser/Code/RMG-Py/rmg.py input.py'" | ||
| echo " - Runs the RMG program with 'input.py' using Python in the Julia environment." | ||
| echo "" | ||
| echo "4. deact ='micromamba deactivate'" | ||
| echo " - Deactivates the current Micromamba environment." | ||
| echo "" | ||
| echo "5. rmgcode='cd /home/rmguser/Code/RMG-Py/'" | ||
| echo " - Changes the current directory to the RMG-Py code directory." | ||
| echo "" | ||
| echo "6. rmgdb ='cd /home/rmguser/Code/RMG-database/" | ||
| echo " - Changes the current directory to the RMG database directory." | ||
| echo "" | ||
| echo "7. arcode ='cd /home/rmguser/Code/ARC'" | ||
| echo " - Changes the current directory to the ARC code directory." | ||
| echo "" | ||
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| # Execute the command specified as CMD in Dockerfile, or the command passed to docker run | ||
| exec "$@" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/bin/bash | ||
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| # Function to initialize Micromamba | ||
| initialize_micromamba() { | ||
| eval "$(micromamba shell hook --shell bash)" | ||
| } | ||
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| # Function to check and adjust permissions for mounted directories | ||
| check_and_adjust_permissions() { | ||
| # Loop through all mounted directories | ||
| for dir in /home/rmguser/*; do | ||
| # Check if it's a directory | ||
| if [ -d "$dir" ]; then | ||
| # Adjust permissions for the directory | ||
| chown -R rmguser:rmguser "$dir" | ||
| fi | ||
| done | ||
| } | ||
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| # Function to run for interactive mode | ||
| run_interactive() { | ||
| check_and_adjust_permissions | ||
| echo "Container started in interactive mode" | ||
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| /home/rmguser/alias_print.sh | ||
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| /bin/bash | ||
| } | ||
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| # Function to run for non-interactive mode | ||
| run_non_interactive() { | ||
| check_and_adjust_permissions | ||
| echo "Container started in non-interactive mode" | ||
| initialize_micromamba | ||
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| case "$1" in | ||
| rmg) | ||
| # Activate rmg_env and run RMG with python-jl | ||
| echo "Running with RMG environment..." | ||
| micromamba activate rmg_env | ||
| python-jl /home/rmguser/Code/RMG-Py/rmg.py "$2" | ||
| ;; | ||
| arc) | ||
| # Activate arc_env and run ARC | ||
| echo "Running with ARC environment..." | ||
| micromamba activate arc_env | ||
| python /home/rmguser/Code/ARC/ARC.py "$2" | ||
| ;; | ||
| *) | ||
| echo "Invalid option. Please specify 'rmg' or 'arc' as the first argument." | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| } | ||
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| # Check if the container is run in interactive mode | ||
| if [ -t 0 ] && [ -t 1 ]; then | ||
| run_interactive | ||
| else | ||
| run_non_interactive "$@" | ||
| fi |