From 2a71397f17c45f465d8a91228bf301158d984d45 Mon Sep 17 00:00:00 2001
From: Benjamin Blankenmeister <b.p.blankenmeister@gmail.com>
Date: Wed, 10 Jan 2024 11:25:06 -0500
Subject: [PATCH] annotations in mem (#33)

* annotations in mem

* Bump version
---
 charts/hail-search/Chart.yaml  | 2 +-
 charts/hail-search/values.yaml | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/charts/hail-search/Chart.yaml b/charts/hail-search/Chart.yaml
index 0c53b373..499fa65e 100644
--- a/charts/hail-search/Chart.yaml
+++ b/charts/hail-search/Chart.yaml
@@ -21,7 +21,7 @@ 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: 0.1.22
+version: 0.1.23
 
 # 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
diff --git a/charts/hail-search/values.yaml b/charts/hail-search/values.yaml
index 12701816..83a96f4f 100644
--- a/charts/hail-search/values.yaml
+++ b/charts/hail-search/values.yaml
@@ -39,7 +39,7 @@ initContainers: |-
   {{ if $version }}
   - name: mkdir-{{ $path | replace "/" "-" | replace "_" "-" | lower}}
     image: busybox:1.35
-    command: ['/bin/mkdir', '-p', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}']
+    command: ['/bin/mkdir', '-p', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}/annotations.ht']
     volumeMounts:
       - mountPath: {{ $.Values.environment.DATASETS_DIR }}
         name: datasets
@@ -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', '-x', '.*families.*', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}']
+    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"}}']
     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', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}/families', '{{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}/families']
+    command: ['gsutil', '-m', 'rsync', '-r', '-x', '.*families.*', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}', '{{ $.Values.environment.SSD_DATASETS_DIR }}/{{ $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES"}}']
     volumeMounts:
       - mountPath: {{ $.Values.environment.SSD_DATASETS_DIR }}
         name: ssd-datasets