updated miniconda env in ci.yml

.github/workflows/ci.yml

@@ -19,11 +19,22 @@ jobs:
         with:
           key: ${{ github.ref }}
           path: .cache
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          channels: conda-forge, bioconda
+          activate-environment: roadies_env_test
+          environment-file: test/roadies_env_test.yaml
       - run: pip install mkdocs-material
       - run: pip install "mkdocs-material[imaging]"
+      - shell: bash -el {0}
+      - run: |
+          ${HOME}/conda/etc/profile.d/conda.sh
+          ${HOME}/conda/etc/profile.d/mamba.sh
+          conda activate roadies_env_test
       - run: |
-          chmod +x roadies_env.sh
-          ./roadies_env.sh
-          pip3 install ete3 numpy snakemake
+          chmod +x test/roadies_env_test.sh
+          ./test/roadies_env_test.sh
+          pip3 install ete3 numpy
           python run_roadies.py --cores 32 --config test/test_config.yaml --mode accurate
       - run: mkdocs gh-deploy --force

test/roadies_env_test.sh

@@ -0,0 +1,31 @@
+#!/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
+
+# 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 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"

test/roadies_env_test.yml

@@ -0,0 +1,18 @@
+name: roadies_env_test
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - 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
+  - ete3