From 5bd896997034fb4d58b1c1951e6b626fe10d16ae Mon Sep 17 00:00:00 2001
From: Dhatri Badri <56312676+dhatribadri@users.noreply.github.com>
Date: Fri, 6 Dec 2024 12:14:53 -0500
Subject: [PATCH] Troubleshoot singularity container test_pipeline.yml

---
 .github/workflows/test_pipeline.yml | 36 +++++++++++++++++------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test_pipeline.yml b/.github/workflows/test_pipeline.yml
index 3ae7b93..41e606a 100644
--- a/.github/workflows/test_pipeline.yml
+++ b/.github/workflows/test_pipeline.yml
@@ -56,8 +56,8 @@ jobs:
       - name: Install dependencies for Singularity
         run: |
           sudo apt-get update
-          sudo apt-get install -y squashfuse fuse2fs gocryptfs
-      
+          sudo apt-get install squashfuse fuse2fs gocryptfs
+
       - name: Set up sysctl for unprivileged user namespaces
         run: |
           sudo sh -c 'echo kernel.unprivileged_userns_clone=1 > /etc/sysctl.d/90-unprivileged_userns.conf'
@@ -67,11 +67,11 @@ jobs:
           sudo sh -c 'cat /proc/sys/kernel/unprivileged_userns_clone'
           sudo sh -c 'ls /etc/sysctl.d/90-unprivileged_userns.conf'
 
-      # - name: Verify Singularity capabilities
-      #   run: |
-      #     singularity build --sandbox docker://ubuntu:20.04
-      #     singularity exec --userns docker://ubuntu:20.04 uname -a
-      #     singularity exec --userns docker://ubuntu:20.04 cat /proc/sys/kernel/unprivileged_userns_clone
+      - name: Verify Singularity capabilities
+        run: |
+          singularity build --sandbox ubuntu_sandbox docker://ubuntu:20.04
+          singularity exec --userns ubuntu_sandbox uname -a
+          singularity exec --userns ubuntu_sandbox cat /proc/sys/kernel/unprivileged_userns_clone
       
       # # Debugging step: Print environment variables 
       # - name: Print environment variables
@@ -97,13 +97,19 @@ jobs:
           mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/quality_raw
           mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/trimmomatic
           mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/raw_coverage
+          
+      - name: SSh into Actions
+        uses: actions/checkout@v4
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
 
       - name: Snakemake workflow
-        # run: |
-        #   snakemake -s QCD.smk -p --use-conda --use-singularity -j 999 --conda-frontend conda --cluster-config config/cluster.json --configfile config/config.yaml --latency-wait 1000 --cores 4 
-        uses: snakemake/snakemake-github-action@v1.25.1
-        with:
-          directory: '.'
-          snakefile: 'QCD.smk'
-          args: '--cores 4 --use-conda --use-singularity --use-envmodules --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --singularity-args "--userns"'
-        #run: echo "🍏 This job's status is ${{ job.status }}."
+        run: |
+          snakemake -s QCD.smk -p --use-conda --use-singularity -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 --singularity-args "--userns"
+        #uses: snakemake/snakemake-github-action@v1.25.1
+        # with:
+        #   directory: '.'
+        #   snakefile: 'QCD.smk'
+        #   #stagein: singularity run docker://alpine cat /etc/os-release
+        #   args: '--cores 4 --use-conda --use-singularity --use-envmodules --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --singularity-args "--userns"'
+        # #run: echo "🍏 This job's status is ${{ job.status }}."