WSL Command Reference

wsl                          # Launch Ubuntu shell
wsl --list                   # Show installed Linux distributions
wsl --shutdown               # Terminate all Linux instances
wsl -l -v                    # Display version and state of each distribution

Core Linux File Commands

Directory Navigation

cd /home/user              # Navigate to specified home directory
cd ..                      # Move to parent directory
cd ../..                   # Jump up two directory levels
cd                         # Return to user's home directory
cd ~username               # Access another user's home directory
cd -                       # Switch to previous working directory
pwd                        # Print current directory path

File and Directory Listing

ls                         # Display directory contents
ls -F                      # Show files with type indicators
ls -l                      # List with permissions, size, and timestamps
ls -a                      # Include hidden files
ls *[0-9]*                 # Filter files containing digits
tree                       # Render directory structure hierarchically
lstree                     # Alternative tree display

Create and Delete Operations

mkdir new_directory                  # Create single directory
mkdir dir1 dir2                      # Create multiple directories
mkdir -p /path/to/nested/dir         # Build complete directory tree
rm -f filename                       # Force remove file
rmdir old_directory                  # Remove empty directory
rm -rf target_directory              # Remove directory with contents
rm -rf dir1 dir2                     # Batch remove directories

Copy, Move, and Link Commands

mv oldname newname                   # Rename or relocate item
cp source.txt destination.txt        # Duplicate file
cp /source/* .                       # Copy all files from source
cp -r /tmp/source .                  # Recursively copy directory
cp -a dir1 dir2                      # Archive copy preserving attributes
ln -s /path/to/file link             # Create symbolic link
ln /path/to/file hardlink            # Create hard link
touch -t 202412011200 filename       # Update file timestamp
iconv -l                             # List supported encodings

File Search Operations

find / -name target                  # Search from root filesystem
find / -user username                # Find files owned by user
find /home/user -name "*.bin"        # Pattern matching in specific path
find /usr/bin -type f -atime +90     # Find executables unused for 90+ days
find /usr/bin -type f -mtime -7      # Locate files modified within week
find / -name "*.rpm" -exec chmod 755 '{}' \;  # Search and modify permissions
find / -xdev -name "*.rpm"           # Exclude removable media from search
locate "*.ps"                        # Quick filename lookup in database
whereis binary_name                  # Locate binary, source, and manual pages
which executable                     # Show full path of executable

Desktop Environment Configuration

Xfce4 with VcXsrv

After launching VcXsrv X Server on Windows, initialize the graphical environment:

startxfce4

Conda Environment Management

Virtual Environment Operations

# List all available environments
conda info --env

# Initialize new environment with specific Python version
conda create --name myenv python=3.9

# Create environment with predefined packages
conda create --name dataenv python=3.8 pandas matplotlib

# Activate environment for use
conda activate myenv

# Exit current environment
conda deactivate

# Duplicate existing environment
conda create --name clone_env --clone original_env

# Permanently remove environment
conda remove --name oldenv --all

# Export environment specification
conda env export > environment.yml

# Reconstruct environment from file
conda env create -f environment.yml

Package Management

# Display installed packages in current environment
conda list

# List packages in specific environment
conda list -n customenv

# Search for available packages
conda search tensorflow

# Install package (optionally with version constraint)
conda install numpy
conda install scipy=1.10.0

# Install into non-active environment
conda install --name targetenv pkg_name

# Refresh installed packages
conda update --all
conda update scipy

# Update package in specific environment
conda update -n targetenv package_name

# Remove packages
conda remove scipy
conda remove -n targetenv package_name

# Clear cached packages
conda clean -p

Scientific Visualization Tools

PyMOL

pymol

Start the PyMOL-Rosetta integration server within PyMOL:

run PyMOLRosettaServer.py

Jupyter Notebook

jupyter notebook

PyRosetta Entegration

Refer to the official PyRosetta documentation for notebook examples:

https://rosettacommons.github.io/PyRosetta.notebooks/