update quicktest.yaml

taha-abdullah · Jun 5, 2024 · dcbb55c · dcbb55c
1 parent b0445ca
commit dcbb55c
Showing 1 changed file with 46 additions and 46 deletions.
diff --git a/.github/workflows/quicktest.yaml b/.github/workflows/quicktest.yaml
@@ -55,54 +55,54 @@ jobs:
           cd $PYTHONPATH
         fi
 
-#  # Run FastSurfer on MRI data
-#  run-fastsurfer:
-#    runs-on: self-hosted
-#    needs: build-singularity-image
-#    steps:
-#    - name: Run FastSurfer
-#      run: |
-#        cd $RUNNER_FS_OUTPUT
-#        DIRECTORY="subjectX"
-#        echo "pwd: $(pwd)"
-#        if [ ! -d "$DIRECTORY" ]; then
-#        # if the directory does not exist, run FastSurfer
-#          echo "Output directory does not exist. Running FastSurfer."
-#          singularity exec --nv \
-#                        --no-home \
-#                        --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
-#                        --env FASTSURFER_HOME=/fastsurfer-dev \
-#                        -B $RUNNER_FS_MRI_DATA:/data \
-#                        -B $RUNNER_FS_OUTPUT:/output \
-#                        -B $RUNNER_FS_LICENSE:/fs_license \
-#                        $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
-#                        /fastsurfer/run_fastsurfer.sh \
-#                        --fs_license /fs_license/.license \
-#                        --t1 /data/subjectx/orig.mgz \
-#                        --sid subjectX --sd /output \
-#                        --parallel --3T
-#        else
-#          echo "Output directory already exists. Deleting directory and running FastSurfer."
-#          rm -rf $DIRECTORY
-#          singularity exec --nv \
-#            --no-home \
-#            --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
-#            --env FASTSURFER_HOME=/fastsurfer-dev \
-#            -B $RUNNER_FS_MRI_DATA:/data \
-#            -B $RUNNER_FS_OUTPUT:/output \
-#            -B $RUNNER_FS_LICENSE:/fs_license \
-#            $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
-#            /fastsurfer/run_fastsurfer.sh \
-#            --fs_license /fs_license/.license \
-#            --t1 /data/subjectx/orig.mgz \
-#            --sid subjectX --sd /output \
-#            --parallel --3T
-#        fi
+  # Run FastSurfer on MRI data
+  run-fastsurfer:
+    runs-on: self-hosted
+    needs: build-singularity-image
+    steps:
+    - name: Run FastSurfer
+      run: |
+        cd $RUNNER_FS_OUTPUT
+        DIRECTORY="subjectX"
+        echo "pwd: $(pwd)"
+        if [ ! -d "$DIRECTORY" ]; then
+        # if the directory does not exist, run FastSurfer
+          echo "Output directory does not exist. Running FastSurfer."
+          singularity exec --nv \
+                        --no-home \
+                        --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
+                        --env FASTSURFER_HOME=/fastsurfer-dev \
+                        -B $RUNNER_FS_MRI_DATA:/data \
+                        -B $RUNNER_FS_OUTPUT:/output \
+                        -B $RUNNER_FS_LICENSE:/fs_license \
+                        $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
+                        /fastsurfer/run_fastsurfer.sh \
+                        --fs_license /fs_license/.license \
+                        --t1 /data/subjectx/orig.mgz \
+                        --sid subjectX --sd /output \
+                        --parallel --3T
+        else
+          echo "Output directory already exists. Deleting directory and running FastSurfer."
+          rm -rf $DIRECTORY
+          singularity exec --nv \
+            --no-home \
+            --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
+            --env FASTSURFER_HOME=/fastsurfer-dev \
+            -B $RUNNER_FS_MRI_DATA:/data \
+            -B $RUNNER_FS_OUTPUT:/output \
+            -B $RUNNER_FS_LICENSE:/fs_license \
+            $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
+            /fastsurfer/run_fastsurfer.sh \
+            --fs_license /fs_license/.license \
+            --t1 /data/subjectx/orig.mgz \
+            --sid subjectX --sd /output \
+            --parallel --3T
+        fi
 
   # Test file existence
   test-file-existence:
     runs-on: self-hosted
-#    needs: run-fastsurfer
+    needs: run-fastsurfer
     steps:
     - name: Test File Existence
       run: |
@@ -111,7 +111,7 @@ jobs:
   # Test for errors in log files
   test-error-messages:
     runs-on: self-hosted
-#    needs: [run-fastsurfer, test-file-existence]
+    needs: [run-fastsurfer, test-file-existence]
     steps:
     - name: Test Log Files For Error Messages
       run: |
@@ -120,7 +120,7 @@ jobs:
   # Test seg_stats
   test-seg-stats:
     runs-on: self-hosted
-#    needs: [run-fastsurfer, test-file-existence, test-error-messages]
+    needs: [run-fastsurfer, test-file-existence, test-error-messages]
     steps:
     - name: Test seg_stats
       run: |