Fix sync annotations command structure

broadinstitute · Apr 3, 2024 · f998be9 · f998be9
1 parent b314b34
commit f998be9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/charts/hail-search/Chart.yaml b/charts/hail-search/Chart.yaml
@@ -19,7 +19,7 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.1.40
+version: 0.1.41
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.

diff --git a/charts/hail-search/values.yaml b/charts/hail-search/values.yaml
@@ -46,7 +46,7 @@ initContainers: |-
   {{- $localPath := $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES" -}}
   - name: sync-annotations-{{ $path | replace "/" "-" | replace "_" "-" | lower}}
     image: busybox:1.35
-    command: ['mkdir', '-p', '{{ $.Values.environment.DATASETS_DIR }}/{{ $localPath }}', '&&', 'rsync', '-r', '{{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $localPath }}/annotations.ht', '{{ $.Values.environment.DATASETS_DIR }}/{{ $localPath }}/annotations.ht']
+    command: ['/bin/bash', '-c', 'mkdir -p {{ $.Values.environment.DATASETS_DIR }}/{{ $localPath }} && rsync -r {{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $localPath }}/annotations.ht {{ $.Values.environment.DATASETS_DIR }}/{{ $localPath }}/annotations.ht']
     volumeMounts:
       - mountPath: {{ $.Values.environment.DATASETS_DIR }}
         name: datasets