altered conda environment

ssi-dk · Oct 24, 2024 · b248b5d · b248b5d
1 parent 4bcff79
commit b248b5d
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Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/.github/workflows/cdiff_fbi_workflow.yml b/.github/workflows/cdiff_fbi_workflow.yml
@@ -27,14 +27,11 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
+          environment-file: environment.yml
+          activate-environment: cdiff_pipeline
           python-version: ${{ matrix.python-version }}
 
-      # step 3: Create the conda environment manually
-      - name: Create conda environment
-        run: |
-          conda create --name cdiff_pipeline picard gatk4 biopython ruamel.yaml kraken bwa samtools
-
-      # step 4
+      # step 3
       - name: Run test script
         run: |
           conda activate cdiff_pipeline

diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,17 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.11
+  - picard
+  - gatk4
+  - kraken
+  - bwa 
+  - samtools
+  - ruamel.yaml
+  - git
+  - pip
+  - pip:
+      - biopython
+      - pytest