Create a setup.sh script for easier instalation

README.md

@@ -9,24 +9,18 @@ If you find Chainsaw useful in your research, please cite:
 
 Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Brooks Paige and Christine Orengo
 
-[bioRxiv](https://doi.org/10.1101/2023.07.19.549732)
+[Bioinformatics](https://doi.org/10.1093/bioinformatics/btae296)
 
 ## Installation
-
-1) install stride: source code and instructions are packaged in this repository in the
-    `stride` directory.  You will need to compile stride and put the executable in your
-    path. Update the `STRIDE_EXE` variable in `src/constants.py` to point to the stride
-    executable.
-
-2) install the python dependencies: `pip install -r requirements.txt`
-
-3) test it's working by running `python get_predictions.py --structure_file example_files/AF-A0A1W2PQ64-F1-model_v4.pdb --output results/test.tsv`
-    by default the output will be saved in the `results` directory.
+Ensure that python 3.8, 3.9, 3.10, or 3.11 is installed, then install dependencies with 
+the command `bash setup.sh`
 
 Optional:
 To visualise the domain assignments, ensure that you have pymol installed and update the
 `PYMOL_EXE` variable in `src/constants.py` to point to the pymol executable.
 
+Chainsaw is tested on Linux and MacOS. It may work on Windows but this is not guaranteed.
+
 ## Usage
 `python get_predictions.py --structure_file /path/to/file.pdb`
 or
@@ -35,3 +29,14 @@ or
 Note that the output predicted boundaries are based on residue consecutive indexing
 starting from 1 (not based on pdb auth numbers).
 
+## Installation Troubleshooting
+If setup.sh fails follow the instructions below:
+
+1) install stride: source code and instructions are packaged in this repository in the
+    `stride` directory. See stride/README_stride for instructions. 
+
+2) install the python dependencies: `pip install -r requirements.txt`
+
+3) test it's working by running `python get_predictions.py --structure_file example_files/AF-A0A1W2PQ64-F1-model_v4.pdb --output results/test.tsv`
+    by default the output will be saved in the `results` directory.
+

setup.sh

@@ -0,0 +1,135 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+STRIDE_DIR="${SCRIPT_DIR}/stride"
+
+# Function to check if a command exists
+command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
+# Function to install build tools
+install_build_tools() {
+    if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+        # Linux
+        if command_exists apt-get; then
+            sudo apt-get update
+            sudo apt-get install -y build-essential
+        elif command_exists yum; then
+            sudo yum groupinstall -y "Development Tools"
+        else
+            echo "Error: Unsupported package manager. Please install build tools manually."
+            return 1
+        fi
+    elif [[ "$OSTYPE" == "darwin"* ]]; then
+        # macOS
+        if ! command_exists gcc || ! command_exists make; then
+            echo "Installing Xcode Command Line Tools..."
+            xcode-select --install
+            read -p "Press enter after Xcode Command Line Tools installation is complete"
+        fi
+    elif [[ "$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" ]]; then
+        # Windows (Git Bash or Cygwin)
+        if ! command_exists gcc || ! command_exists make; then
+            echo "Please install MinGW-w64 or Cygwin with gcc and make."
+            echo "Visit: https://sourceforge.net/projects/mingw-w64/ or https://www.cygwin.com/"
+            return 1
+        fi
+    else
+        echo "Unsupported operating system"
+        return 1
+    fi
+    return 0
+}
+
+# Function to compile stride
+compile_stride() {
+    echo "Starting stride compilation process..."
+
+    # Decompress stride
+    if [ -f "$STRIDE_DIR/stride.tgz" ]; then
+        echo "Decompressing stride..."
+        tar -zxf "$STRIDE_DIR/stride.tgz" -C "$STRIDE_DIR" || return 1
+    else
+        echo "Error: stride.tgz not found in $STRIDE_DIR"
+        return 1
+    fi
+
+    # Install build tools if necessary
+    echo "Checking and installing build tools if necessary..."
+    install_build_tools || return 1
+
+    # Compile stride
+    echo "Compiling stride..."
+    cd "$STRIDE_DIR" || return 1
+    make || return 1
+
+    # Change permissions
+    echo "Changing stride permissions to executable..."
+    chmod +x stride || return 1
+
+    # Test run
+    echo "Performing a test run of stride..."
+    ./stride --help || return 1
+
+    # Change back to the original directory
+    cd - || return 1
+
+    echo "Stride compilation successful!"
+    return 0
+}
+
+# Main script execution starts here
+
+# Check if venv directory chswEnv exists
+if [ ! -d "$SCRIPT_DIR/chswEnv" ]; then
+    echo "Creating virtual environment..."
+    if [[ "$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" ]]; then
+       python -m venv "$SCRIPT_DIR/chswEnv"
+    # Try Python 3.11, then 3.10, then 3.9
+    elif command_exists python3.11; then
+        python3.11 -m venv "$SCRIPT_DIR/chswEnv"
+        echo "Created virtual environment with Python 3.11"
+    elif command_exists python3.10; then
+        python3.10 -m venv "$SCRIPT_DIR/chswEnv"
+        echo "Created virtual environment with Python 3.10"
+    elif command_exists python3.9; then
+        python3.9 -m venv "$SCRIPT_DIR/chswEnv"
+        echo "Created virtual environment with Python 3.9"
+    elif command_exists python3.8; then
+        python3.9 -m venv "$SCRIPT_DIR/chswEnv"
+        echo "Created virtual environment with Python 3.8"
+    else
+        echo "Error: Python 3.8, 3.9, 3.10, or 3.11 is not installed. Please install one of these versions and try again."
+        exit 1
+    fi
+else
+    echo "Virtual environment already exists."
+fi
+
+# Activate the virtual environment
+if [[ "$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" ]]; then
+    source "$SCRIPT_DIR/chswEnv/Scripts/activate"
+else
+    source "$SCRIPT_DIR/chswEnv/bin/activate"
+fi
+
+echo "Upgrading pip..."
+pip install --upgrade pip
+echo "Installing dependencies from requirements.txt..."
+pip install -r "$SCRIPT_DIR/requirements.txt"
+
+# Compile stride
+if compile_stride; then
+    echo "Stride compilation and setup completed successfully."
+    echo "Chainsaw setup complete. Test the installation by running the following command:"
+    echo "python get_predictions.py --structure_file example_files/AF-A0A1W2PQ64-F1-model_v4.pdb --output results/test.tsv"
+else
+    echo "Error occurred during stride compilation."
+    echo "Please compile stride manually by following these steps:"
+    echo "1. Navigate to the stride directory: cd $STRIDE_DIR"
+    echo "2. Decompress the source: tar -zxf stride.tgz"
+    echo "3. Compile the source: make"
+    echo "4. Make the binary executable: chmod +x stride"
+    echo "5. Test the binary: ./stride --help"
+fi