rearrange env and add docker authentication

ktmeaton · Oct 13, 2020 · 787cb51 · 787cb51
1 parent a8e3ae4
commit 787cb51
Showing 1 changed file with 10 additions and 7 deletions.
diff --git a/.github/workflows/install.yaml b/.github/workflows/install.yaml
@@ -1,13 +1,6 @@
 #------------------------------------------------------------------------------#
 name: Install
 #------------------------------------------------------------------------------#
-# Global workflow environment variables
-env:
-    CONDA_ENVS_PATH: "/home/runner/miniconda/envs:/usr/share/miniconda/envs"
-    CONDA_PKGS_DIRS: "/home/runner/miniconda/pkgs"
-    CONDA_SNK_PREFIX: "/home/runner/work/plague-phylogeography/plague-phylogeography/.snakemake/conda"
-    SINGULARITY_SNK_PREFIX: "/home/runner/work/plague-phylogeography/plague-phylogeography/.snakemake/singularity/"
-#------------------------------------------------------------------------------#
 # Workflow conditions
 on:
   push:
@@ -33,6 +26,16 @@ jobs:
       fail-fast: false
     steps:
       #------------------------------------------------------------------------#
+      # Env setup
+      - name: setup environment variables
+        run: |
+          echo "CONDA_ENVS_PATH=/home/runner/miniconda/envs:/usr/share/miniconda/envs" >> $GITHUB_ENV
+          echo "CONDA_PKGS_DIRS=/home/runner/miniconda/pkgs" >> $GITHUB_ENV
+          echo "CONDA_SNK_PREFIX=/home/runner/work/plague-phylogeography/plague-phylogeography/.snakemake/conda" >> $GITHUB_ENV
+          echo "SINGULARITY_SNK_PREFIX=/home/runner/work/plague-phylogeography/plague-phylogeography/.snakemake/singularity/" >> $GITHUB_ENV
+          echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV
+          echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV
+      #------------------------------------------------------------------------#
       # Checkout Repository
       - name: checkout repo
         uses: actions/checkout@v2