fix Clustal Omega and MAFFT installation

CDDLeiden · Jan 5, 2024 · b07443d · b07443d
1 parent ae3504a
commit b07443d
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/.github/workflows/dev_ci.yml b/.github/workflows/dev_ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.10',' 3.11',' 3.12']
+        python-version: ['3.10',' 3.11']
     defaults:
       run:
         shell: bash
@@ -23,14 +23,19 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install External Software
+    - name: Install Clustal Omega and MAFFT
       run: |
-        wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
-        wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+        if [ "${{ runner.os }}" = "macOS" ]; then
+          wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo
+          wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-signed.pkg -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+        elif [ "${{ runner.os }}" = "Linux" ]; then
+          wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
+          wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+        fi
         export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
         export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
         clustalo --version  # For debugging clustalo version

diff --git a/.github/workflows/pre_merge_ci.yml b/.github/workflows/pre_merge_ci.yml
@@ -19,7 +19,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
 
@@ -31,7 +31,7 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
 
-    - name: Install External Software
+    - name: Install Clustal Omega and MAFFT
       run: |
         wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
         wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft