fix: snakemake and mamba deployment (#978)

.github/workflows/main.yml

@@ -34,28 +34,30 @@ jobs:
           submodules: recursive
           fetch-depth: 0
 
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: snakemake
+          channels: "conda-forge, bioconda"
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+
       - name: Setup Snakemake environment
+        shell: bash -el {0}
         run: |
-          # ensure that mamba is happy to write into the cache
-          sudo chown -R runner:docker /usr/share/miniconda/pkgs/cache
-          conda install -c conda-forge mamba --quiet
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          mamba create -c bioconda -c conda-forge --quiet -y --name snakemake snakemake-minimal pytest
           conda config --set channel_priority strict
+          mamba install -n snakemake -y snakemake-minimal pytest
 
       - name: Fetch master
         if: github.ref != 'refs/heads/master'
         run: |
           git fetch origin master
 
       - name: Run tests
+        shell: bash -el {0}
         env:
           DIFF_MASTER: ${{ github.event_name == 'pull_request' }}
           DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/master' }}
         run: |
-          # activate conda env
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate snakemake
-
           # run tests
           pytest test.py -v

.github/workflows/qc.yml

@@ -8,45 +8,60 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
+
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: fmt
+          channels: "conda-forge, bioconda"
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
 
       - name: Setup environment
-        run: conda create --quiet -c bioconda -c conda-forge --name fmt black snakefmt
+        shell: bash -el {0}
+        run: |
+          conda config --set channel_priority strict
+          mamba install -n fmt -y black snakefmt
 
       - name: Check Python formatting
+        shell: bash -el {0}
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate fmt
           black --check */*/*/wrapper.py */*/wrapper.py
-      
+
       # TODO reactivate once comment errors are fixed
       # - name: Check Snakemake formatting
       #   run: |
       #     export PATH="/usr/share/miniconda/bin:$PATH"
       #     source activate fmt
       #     snakefmt --check $(git diff origin/master --name-only | grep Snakefile)
-  
+
   linting:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
 
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: snakemake
+          channels: "conda-forge, bioconda"
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+
       - name: Setup Snakemake environment
+        shell: bash -el {0}
         run: |
-          # ensure that mamba is happy to write into the cache
-          sudo chown -R runner:docker /usr/share/miniconda/pkgs/cache
-          conda install -c conda-forge mamba --quiet
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          mamba create -c bioconda -c conda-forge --quiet -y --name snakemake snakemake-minimal
-      
+          conda config --set channel_priority strict
+          mamba install -n snakemake -y snakemake-minimal snakemake
+
       - name: Fetch master
         run: |
           git fetch origin master
 
       - name: Linting
+        shell: bash -el {0}
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate snakemake
           declare -i ERRORS=0
           # get all modified and added files, not those that are deleted
           for f in $(git diff origin/master --name-only --diff-filter=d | grep Snakefile)

test.py

@@ -3169,18 +3169,16 @@ def test_star_align():
     os.makedirs("bio/star/align/test/index", exist_ok=True)
     try:
         subprocess.check_call(
-            "conda env create " "--file bio/star/align/environment.yaml " "-n star-env",
+            "mamba env create --file bio/star/align/environment.yaml -n star-env",
             shell=True,
-            executable="/bin/bash",
         )
         subprocess.check_call(
-            "source activate star-env; STAR --genomeDir "
+            "bash -l -c 'source $(dirname $(dirname $(which mamba)))/bin/activate star-env; STAR --genomeDir "
             "bio/star/align/test/index "
             "--genomeFastaFiles bio/star/align/test/genome.fasta "
             "--runMode genomeGenerate "
-            "--genomeSAindexNbases 8",
+            "--genomeSAindexNbases 8'",
             shell=True,
-            executable="/bin/bash",
         )
     finally:
         shutil.rmtree("star-env", ignore_errors=True)