remove debugging, configure pipelin

ktmeaton · Oct 13, 2020 · 8f98d7c · 8f98d7c
1 parent 490e1e3
commit 8f98d7c
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Showing 2 changed files with 28 additions and 25 deletions.
diff --git a/.github/workflows/install.yaml b/.github/workflows/install.yaml
@@ -31,10 +31,6 @@ jobs:
         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 }}" >> $GITHUB_ENV
       #------------------------------------------------------------------------#
       # Checkout Repository
       - name: checkout repo
@@ -58,15 +54,21 @@ jobs:
           conda activate plague-phylogeography;
           snakemake --profile profiles/gh-actions help;
       #------------------------------------------------------------------------#
-      - name: Setup tmate session
-        uses: mxschmitt/action-tmate@v3
+      #- name: Setup tmate session
+      #  uses: mxschmitt/action-tmate@v3
   #----------------------------------------------------------------------------#
   install_singularity:
     name: Install with Singularity
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
+      #------------------------------------------------------------------------#
+      - name: setup environment variables
+        run: |
+          echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV
+          echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV
+      #SINGULARITY_ROOT: /opt/hostedtoolcache/singularity/3.6.3/x64
       #------------------------------------------------------------------------#
       # Checkout Repository
       - name: checkout repo
@@ -92,10 +94,5 @@ jobs:
         run: |
           singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions help;
       #------------------------------------------------------------------------#
-      - name: Setup tmate session
-        uses: mxschmitt/action-tmate@v3
-      #------------------------------------------------------------------------#
-      # run help
-      #- name: configure sra-toolkit
-      #  run: |
-      #    singularity exec plague-phylogeography_dev.sif vdb-config --interactive --interactive-mode textual;
+      #- name: Setup tmate session
+      #  uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/pipeline.yaml b/.github/workflows/pipeline.yaml
@@ -3,10 +3,6 @@ name: Pipeline CI
 #------------------------------------------------------------------------------#
 # 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/"
     TEST_DOWNLOAD: "test_download_reference test_download_assembly test_download_sra test_download_gff test_download_gbff"
     TEST_EAGER: "test_eager_local test_eager_sra"
     TEST_SNIPPY: "test_snippy_pairwise_assembly test_snippy_pairwise_sra test_snippy_pairwise_local"
@@ -45,6 +41,12 @@ jobs:
     timeout-minutes: 120
     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
+      #------------------------------------------------------------------------#
       # Checkout Repository
       - name: checkout repo
         uses: actions/checkout@v2
@@ -65,13 +67,7 @@ jobs:
         shell: bash -l {0}
         run: |
             conda activate plague-phylogeography;
-            snakemake --profile profiles/gh-actions --use-conda --conda-prefix ${CONDA_SNK_PREFIX} ${TEST_DOWNLOAD};
-      # Test eager
-      #- name: test nf-core/eager
-      #  shell: bash -l {0}
-      #  run: |
-      #      conda activate plague-phylogeography;
-      #      snakemake --profile profiles/gh-actions --use-conda --conda-prefix ${CONDA_SNK_PREFIX} ${TEST_EAGER};
+            snakemake --profile profiles/gh-actions ${TEST_DOWNLOAD};
   #----------------------------------------------------------------------------#
   pipeline_singularity:
     name: Pipeline with Singularity
@@ -80,6 +76,11 @@ jobs:
       fail-fast: false
     steps:
       #------------------------------------------------------------------------#
+      - name: setup environment variables
+        run: |
+          echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV
+          echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV
+      #------------------------------------------------------------------------#
       # Checkout Repository
       - name: checkout repo
         uses: actions/checkout@v2
@@ -94,7 +95,12 @@ jobs:
       - name: pull container
         run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev
       #------------------------------------------------------------------------#
+      # Configure sra-toolkit
+      - name: configure sra-toolkit
+        run: |
+          mkdir -p ~/.ncbi/;
+          printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg;
       # test download
       - name: test download
         run: |
-          singularity exec plague-phylogeography_dev.sif snakemake --use-singularity --singularity-prefix ${SINGULARITY_SNK_PREFIX} --profile profiles/gh-actions ${TEST_DOWNLOAD};
+          singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions ${TEST_DOWNLOAD};