From 12984a176ed73bb476f3e0d3d8b5cc28b103e14d Mon Sep 17 00:00:00 2001
From: Glenn032787 <79811082+Glenn032787@users.noreply.github.com>
Date: Fri, 20 Jan 2023 17:44:52 -0500
Subject: [PATCH] Install snakemake and singularity in github action

Follow instructions from https://github.com/snakemake/snakemake-github-action/issues/9
---
 .github/workflows/run_snakemake.yaml | 32 ++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/run_snakemake.yaml b/.github/workflows/run_snakemake.yaml
index fd22ae0..880978f 100644
--- a/.github/workflows/run_snakemake.yaml
+++ b/.github/workflows/run_snakemake.yaml
@@ -10,6 +10,21 @@ jobs:
       - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
       - name: Check out repository code
         uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          conda install -c conda-forge mamba
+      - name: Setup snakemake
+        run: |
+          mamba install -c conda-forge -c bioconda snakemake singularity 
+      - run: echo "Finish installing snakemake"
       - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
       - run: echo "🖥️ The workflow is now ready to test your code on the runner."
       - name: Downlaod hg38 ref file
@@ -21,13 +36,16 @@ jobs:
           unzip example/ref/snpEff_v5_0_GRCh38.99.zip -d example/ref/
           mv example/ref/data example/ref/snpeff
       - run: echo "Reference file downloaded to runner"
-      - name: Testing
-        uses: snakemake/snakemake-github-action@v1
-        with:
-          directory: '.'
-          snakefile: 'Snakefile'
-          args: '-c 2 --use-singularity --configfiles example/config/defaults.yaml example/config/parameters.yaml example/config/samples.yaml'
-          stagein: '' # additional preliminary commands to run (can be multiline)
+      #- name: Testing
+      #  uses: snakemake/snakemake-github-action@v1
+      #  with:
+      #    directory: '.'
+      #    snakefile: 'Snakefile'
+      #    args: '-c 2 --use-singularity --configfiles example/config/defaults.yaml example/config/parameters.yaml example/config/samples.yaml'
+      #    stagein: '' # additional preliminary commands to run (can be multiline)
+      - name: Testin
+        run: | 
+          snakemake -c 2 --use-singularity --configfiles example/config/defaults.yaml example/config/parameters.yaml example/config/samples.yaml 
       - name: Check output
         run: |
           ls -lt output/exampleSample/