updated ci.yaml

.github/workflows/ci.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Run Tests
         run: |
           chmod +x test/roadies_env_test.sh
-          ./test/roadies_env_test.sh
+          source test/roadies_env_test.sh
           pip3 install ete3 six numpy
           pip install PyYAML
           python run_roadies.py --cores 32 --config test/test_config.yaml --mode accurate

test/roadies_env_test.sh

@@ -1,31 +1,93 @@
 #!/bin/bash
 
-sudo apt-get update
-sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git vim screen default-jre libgomp1 libboost-all-dev cmake
+# sudo apt-get update
+# sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git vim screen default-jre libgomp1 libboost-all-dev cmake
 
-# Download ASTER repository
-wget https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip
-unzip Linux.zip
-cd ASTER-Linux
-make
-cd ..
+# # Download ASTER repository
+# wget https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip
+# unzip Linux.zip
+# cd ASTER-Linux
+# make
+# cd ..
 
-# Clone PASTA repository and install
-git clone https://github.com/smirarab/pasta.git
+# # Clone PASTA repository and install
+# git clone https://github.com/smirarab/pasta.git
 
-# Clone Sate-Tools repository
-git clone https://github.com/smirarab/sate-tools-linux.git
+# # Clone Sate-Tools repository
+# git clone https://github.com/smirarab/sate-tools-linux.git
 
-cd pasta
-python3 setup.py develop --user
-cd ..
-
-#build sampling code
-cd workflow/scripts/sampling
-mkdir build
-cd build
-cmake ..
-make
-cd ../../../..
-
-echo "Setup complete"
+# cd pasta
+# python3 setup.py develop --user
+# cd ..
+
+# #build sampling code
+# cd workflow/scripts/sampling
+# mkdir build
+# cd build
+# cmake ..
+# make
+# cd ../../../..
+
+# echo "Setup complete"
+
+#!/bin/bash
+
+# Required installations:
+# sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git vim screen default-jre libgomp1 libboost-all-dev cmake
+
+# Define installation paths and check for directory
+CONDA_PATH="${HOME}/conda"
+ROADIES_ENV_SETUP="roadies_env.sh"
+
+# Download and install Mambaforge if not already installed
+if [ ! -d "${CONDA_PATH}" ]; then
+    wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge-Linux-x86_64.sh
+    bash Mambaforge-Linux-x86_64.sh -b -p "${CONDA_PATH}"
+fi
+
+# Create and setup the Conda environment if it doesn't exist
+source "${CONDA_PATH}/etc/profile.d/conda.sh"  # Temporarily source conda for this script
+source "${CONDA_PATH}/etc/profile.d/mamba.sh"  # Temporarily source mamba for this script
+if ! conda env list | grep -q "roadies_env"; then
+    mamba create -y -c conda-forge -c bioconda --name roadies_env snakemake alive-progress biopython iqtree=2.2.0.3 numpy lastz mashtree matplotlib seaborn treeswift=1.1.28 fasttree=2.1.11 python=3.11 raxml-ng ete3
+fi
+conda activate roadies_env
+
+# Download and setup ASTER repository if not already done
+if [ ! -d "ASTER-Linux" ]; then
+    wget -q https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip -O Linux.zip
+    unzip -q Linux.zip
+    cd ASTER-Linux
+    make
+    g++ -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro2
+    cd ..
+fi
+
+# Clone and setup PASTA if not already done
+if [ ! -d "pasta" ]; then
+    git clone https://github.com/smirarab/pasta.git
+    cd pasta
+    python3 setup.py develop --user
+    cd ..
+fi
+
+# Clone Sate-Tools if not already done
+if [ ! -d "sate-tools-linux" ]; then
+    git clone https://github.com/smirarab/sate-tools-linux.git
+fi
+
+# Build sampling code
+if [ ! -d "workflow/scripts/sampling/build" ]; then
+    cd workflow/scripts/sampling
+    mkdir build
+    cd build
+    cmake ..
+    make
+    cd ../../../..
+fi
+
+# Install ete3 for the user, only if it is not already installed
+python3 -m pip show ete3 &>/dev/null || python3 -m pip install --user ete3
+
+echo "Setup complete. Remember to source '${ROADIES_ENV_SETUP}' before running your projects."
+