Update test_pipeline.yml

Snitkin-Lab-Umich · Dec 6, 2024 · 723023e · 723023e
1 parent 5bd8969
commit 723023e
Showing 1 changed file with 55 additions and 34 deletions.
diff --git a/.github/workflows/test_pipeline.yml b/.github/workflows/test_pipeline.yml
@@ -48,30 +48,49 @@ jobs:
           pip install --upgrade snakemake
         
       - name: Install singularity
-        uses: eWaterCycle/setup-singularity@v7
-        with:
-          singularity-version: 3.8.3
-
-      # Diagnostic steps for Singularity capabilities 
-      - name: Install dependencies for Singularity
         run: |
-          sudo apt-get update
-          sudo apt-get install squashfuse fuse2fs gocryptfs
+          sudo apt-get install -y \
+           autoconf \
+           automake \
+           cryptsetup \
+           fuse \
+           fuse2fs \
+           git \
+           libfuse-dev \
+           libglib2.0-dev \
+           libseccomp-dev \
+           libtool \
+           pkg-config \
+           runc \
+           squashfs-tools \
+           squashfs-tools-ng \
+           uidmap \
+           wget \
+           zlib1g-dev
+      #   uses: eWaterCycle/setup-singularity@v7
+      #   with:
+      #     singularity-version: 3.8.3
 
-      - 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'
-          sudo sysctl -p /etc/sysctl.d/90-unprivileged_userns.conf
-          sudo sysctl --system
-          uname -r
-          sudo sh -c 'cat /proc/sys/kernel/unprivileged_userns_clone'
-          sudo sh -c 'ls /etc/sysctl.d/90-unprivileged_userns.conf'
+      # # Diagnostic steps for Singularity capabilities 
+      # - name: Install dependencies for Singularity
+      #   run: |
+      #     sudo apt-get update
+      #     sudo apt-get install squashfuse fuse2fs gocryptfs
 
-      - 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
+      # - 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'
+      #     sudo sysctl -p /etc/sysctl.d/90-unprivileged_userns.conf
+      #     sudo sysctl --system
+      #     uname -r
+      #     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 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
@@ -98,18 +117,20 @@ jobs:
           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: 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 --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 --singularity-args "--userns"
-        #uses: snakemake/[email protected]
-        # 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 }}."
+        # 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/[email protected]
+        with:
+          directory: '.'
+          snakefile: 'QCD.smk'
+          stagein: ./mconfig --without-suid && \
+                  make -C ./builddir && \
+                  make -C ./builddir install
+          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 }}."