Fix macOS CI - install conda using miniforge (#31)

bcgsc · Oct 3, 2024 · 1a29d35 · 1a29d35
1 parent 7ce1ce0
commit 1a29d35
Showing 1 changed file with 10 additions and 3 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -39,15 +39,22 @@ jobs:
     persistCredentials: true
     submodules: true
 
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
 
   - script: conda create --yes --quiet --name mtgrasp_ci
     displayName: Create Anaconda environment
 
   - script: |
       source activate mtgrasp_ci
-      conda install --yes -c bioconda -c conda-forge python mamba
       mamba install --yes -c conda-forge -c bioconda snakemake 'blast>=2.9.0' biopython seqtk abyss ntjoin bwa samtools pilon ntcard 'mitos>=2.1.7'
     displayName: Install dependencies