added lastz and astral executable

Author: ang037

roadies_env.sh

@@ -19,21 +19,10 @@ source "${CONDA_PATH}/etc/profile.d/conda.sh"  # Temporarily source conda for th
 source "${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
+    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 lastz=1.04.52 aster=1.19 pyyaml seaborn
 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/tags/v1.19.zip -O Linux.zip
-    unzip -q Linux.zip
-    mv ASTER-1.19 ASTER-Linux
-    make
-    g++ -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro3
-    cd ..
-    mv ASTER-Linux/bin/astral-pro3 /usr/local/bin/
-fi
-
 # Clone PASTA if not already done
 if [ ! -d "pasta" ]; then
     git clone https://github.com/smirarab/pasta.git
@@ -64,18 +53,6 @@ if [ ! -d "workflow/scripts/sampling/build" ]; then
     cd ../../../..
 fi
 
-# Download and setup LASTZ if not already done
-if [ ! -d "workflow/scripts/lastz_40" ]; then
-    cd workflow/scripts
-    wget https://github.com/lastz/lastz/archive/refs/tags/1.04.45.zip
-    unzip 1.04.45.zip 
-    cd lastz-1.04.45/src/
-    make lastz_40
-    make install_40
-    cp lastz_40 ../../../../
-    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
 

test/roadies_env_test.sh

@@ -8,17 +8,9 @@ bash Miniforge3.sh -b -p "${HOME}/conda"
 
 source "${HOME}/conda/etc/profile.d/conda.sh"
 source "${HOME}/conda/etc/profile.d/mamba.sh"
+mamba create -y -c conda-forge -c bioconda --name roadies_env_test 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 lastz=1.04.52 aster=1.19 pyyaml seaborn
 conda activate roadies_env_test
 
-wget -q https://github.com/chaoszhang/ASTER/archive/refs/tags/v1.19.zip -O Linux.zip
-unzip -q Linux.zip
-mv ASTER-1.19 ASTER-Linux
-cd ASTER-Linux
-make
-g++ -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro3
-cd ..
-mv ASTER-Linux/bin/astral-pro3 /usr/local/bin/
-
 git clone https://github.com/smirarab/pasta.git
 
 git clone https://github.com/smirarab/sate-tools-linux.git
@@ -35,15 +27,5 @@ cmake ..
 make
 cd ../../../..
 
-# Build LASTZ
-cd workflow/scripts
-wget https://github.com/lastz/lastz/archive/refs/tags/1.04.45.zip
-unzip 1.04.45.zip 
-cd lastz-1.04.45/src/
-make lastz_40
-make install_40
-cp lastz_40 ../../../../
-cd ../../../../
-
 echo "Setup complete. Remember to source before running your projects."