redirect stderr to stdout (#37)

* redirect stderr to stdout * Bump version
broadinstitute · Feb 14, 2024 · 854f92c · 854f92c
1 parent be5e0e0
commit 854f92c
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Showing 2 changed files with 4 additions and 4 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: 0.1.28
+version: 0.1.29
 # 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
@@ -51,13 +51,13 @@ initContainers: |-
         name: ssd-datasets
   - name: sync-{{ $path | replace "/" "-" | replace "_" "-" | lower}}
     image: gcr.io/google.com/cloudsdktool/google-cloud-cli:latest
-    command: ['gsutil', '-m', 'rsync', '-r', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}/annotations.ht', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}/annotations.ht']
+    command: ['gsutil', '-m', 'rsync', '-r', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}/annotations.ht', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}/annotations.ht', '2>&1']
     volumeMounts:
       - mountPath: {{ $.Values.environment.DATASETS_DIR }}
         name: datasets
   - name: sync-ssd-{{ $path | replace "/" "-" | replace "_" "-" | lower}}
     image: gcr.io/google.com/cloudsdktool/google-cloud-cli:latest
-    command: ['gsutil', '-m', 'rsync', '-r', '-x', '.*annotations.*', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}', '{{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}']
+    command: ['gsutil', '-m', 'rsync', '-r', '-x', '.*annotations.*', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}', '{{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}', '2>&1']
     volumeMounts:
       - mountPath: {{ $.Values.environment.SSD_DATASETS_DIR }}
         name: ssd-datasets
@@ -67,7 +67,7 @@ initContainers: |-
   {{- range $query := $queries -}}
   - name: sync-crdq-{{ $path | replace "/" "-" | replace "_" "-" | lower}}-{{ $query | replace "_" "-" | lower}}
     image: gcr.io/google.com/cloudsdktool/google-cloud-cli:latest
-    command: ['gsutil', '-m', 'cp', '-r', '{{ $.Values.sourceCachedReferenceDatasetQueriesDir }}/{{ $path }}/cached_reference_dataset_queries/{{ $query }}.ht', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path }}']
+    command: ['gsutil', '-m', 'cp', '-r', '{{ $.Values.sourceCachedReferenceDatasetQueriesDir }}/{{ $path }}/cached_reference_dataset_queries/{{ $query }}.ht', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path }}', '2>&1']
     volumeMounts:
       - mountPath: {{ $.Values.environment.DATASETS_DIR }}
         name: datasets