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broadinstitute · Oct 9, 2024 · 4ea5657 · 4ea5657
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diff --git a/charts/hail-search/README.md b/charts/hail-search/README.md
@@ -1,6 +1,6 @@
 # hail-search
 
-![Version: 0.2.8-dev](https://img.shields.io/badge/Version-0.2.8--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: f7c9a85e5de3064e65766915a440f298332bf745](https://img.shields.io/badge/AppVersion-f7c9a85e5de3064e65766915a440f298332bf745-informational?style=flat-square)
+![Version: 0.2.9-dev](https://img.shields.io/badge/Version-0.2.9--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: f7c9a85e5de3064e65766915a440f298332bf745](https://img.shields.io/badge/AppVersion-f7c9a85e5de3064e65766915a440f298332bf745-informational?style=flat-square)
 
 A Helm chart for deploying the hail backend of Seqr, an open source software platform for rare disease genomics
 
@@ -19,7 +19,7 @@ A Helm chart for deploying the hail backend of Seqr, an open source software pla
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../lib | lib | 0.1.3 |
+| file://../lib | lib | 0.1.4 |
 
 ## Values
 
@@ -62,7 +62,7 @@ false
 			<td>environment.HAIL_SEARCH_DATA_DIR</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr/seqr-hail-search-data"
+"/var/seqr/seqr-hail-search-data"
 </pre>
 </td>
 			<td></td>
@@ -71,7 +71,7 @@ false
 			<td>environment.REFERENCE_DATASETS_DIR</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr/seqr-reference-data"
+"/var/seqr/seqr-reference-data"
 </pre>
 </td>
 			<td></td>
@@ -197,7 +197,7 @@ true
 			<td>volumeMounts</td>
 			<td>string</td>
 			<td><pre lang="json">
-"- name: seqr-datasets\n  mountPath: /seqr\n  readOnly: true"
+"- name: seqr-datasets\n  mountPath: /var/seqr\n  readOnly: true"
 </pre>
 </td>
 			<td></td>
@@ -242,7 +242,7 @@ true
 			<td>lib.exports.global.lib.persistentVolume.local.path</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>

diff --git a/charts/lib/README.md b/charts/lib/README.md
@@ -1,6 +1,6 @@
 # lib
 
-![Version: 0.1.3](https://img.shields.io/badge/Version-0.1.3-informational?style=flat-square) ![Type: library](https://img.shields.io/badge/Type-library-informational?style=flat-square)
+![Version: 0.1.4](https://img.shields.io/badge/Version-0.1.4-informational?style=flat-square) ![Type: library](https://img.shields.io/badge/Type-library-informational?style=flat-square)
 
 A collection of shared resources used by the composing helm charts of Seqr, an open source software platform for rare disease genomics
 
@@ -55,7 +55,7 @@ A collection of shared resources used by the composing helm charts of Seqr, an o
 			<td>exports.global.lib.persistentVolume.local.path</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>

diff --git a/charts/pipeline-runner/README.md b/charts/pipeline-runner/README.md
@@ -1,6 +1,6 @@
 # pipeline-runner
 
-![Version: 0.1.3-dev](https://img.shields.io/badge/Version-0.1.3--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: e15e33e99648d7a765d1e204bb6c6bc92a40b0f9](https://img.shields.io/badge/AppVersion-e15e33e99648d7a765d1e204bb6c6bc92a40b0f9-informational?style=flat-square)
+![Version: 0.1.4-dev](https://img.shields.io/badge/Version-0.1.4--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: e15e33e99648d7a765d1e204bb6c6bc92a40b0f9](https://img.shields.io/badge/AppVersion-e15e33e99648d7a765d1e204bb6c6bc92a40b0f9-informational?style=flat-square)
 
 A Helm chart for deploying the loading pipeline of Seqr, an open source software platform for rare disease genomics
 
@@ -19,7 +19,7 @@ A Helm chart for deploying the loading pipeline of Seqr, an open source software
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../lib | lib | 0.1.3 |
+| file://../lib | lib | 0.1.4 |
 
 ## Values
 
@@ -260,7 +260,7 @@ true
 			<td>pods[1].initContainers</td>
 			<td>string</td>
 			<td><pre lang="json">
-"- name: mkdir-luigi-state\n  image: busybox:1.35\n  imagePullPolicy: {{ $.Values.image.pullPolicy }}\n  command: ['/bin/mkdir', '-p', '/seqr/luigi-state']\n  {{- with $.Values.volumeMounts }}\n  volumeMounts:\n    {{- tpl . $ | nindent 4 }}\n  {{- end }}"
+"- name: mkdir-luigi-state\n  image: busybox:1.35\n  imagePullPolicy: {{ $.Values.image.pullPolicy }}\n  command: ['/bin/mkdir', '-p', '/var/seqr/luigi-state']\n  {{- with $.Values.volumeMounts }}\n  volumeMounts:\n    {{- tpl . $ | nindent 4 }}\n  {{- end }}"
 </pre>
 </td>
 			<td></td>
@@ -368,7 +368,7 @@ true
 			<td>volumeMounts</td>
 			<td>string</td>
 			<td><pre lang="json">
-"- name: seqr-datasets\n  mountPath: /seqr\n  readOnly: false"
+"- name: seqr-datasets\n  mountPath: /var/seqr\n  readOnly: false"
 </pre>
 </td>
 			<td></td>
@@ -413,7 +413,7 @@ true
 			<td>lib.exports.global.lib.persistentVolume.local.path</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>

diff --git a/charts/seqr-platform/README.md b/charts/seqr-platform/README.md
@@ -1,6 +1,6 @@
 # seqr-platform
 
-![Version: 0.1.3-dev](https://img.shields.io/badge/Version-0.1.3--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square)
+![Version: 0.1.11-dev](https://img.shields.io/badge/Version-0.1.11--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square)
 
 A Helm chart for deploying all components of Seqr, an open source software platform for rare disease genomics
 
@@ -20,10 +20,10 @@ A Helm chart for deploying all components of Seqr, an open source software platf
 
 | Repository | Name | Version |
 |------------|------|---------|
-| https://broadinstitute.github.io/seqr-helm | hail-search | 0.2.8-dev |
-| https://broadinstitute.github.io/seqr-helm | lib | 0.1.3 |
-| https://broadinstitute.github.io/seqr-helm | pipeline-runner | 0.1.2-dev |
-| https://broadinstitute.github.io/seqr-helm | seqr | 1.1.7-dev |
+| https://broadinstitute.github.io/seqr-helm | hail-search | 0.2.9-dev |
+| https://broadinstitute.github.io/seqr-helm | lib | 0.1.4 |
+| https://broadinstitute.github.io/seqr-helm | pipeline-runner | 0.1.4-dev |
+| https://broadinstitute.github.io/seqr-helm | seqr | 1.1.11-dev |
 
 ## Values
 

diff --git a/charts/seqr/README.md b/charts/seqr/README.md
@@ -1,6 +1,6 @@
 # seqr
 
-![Version: 1.1.7-dev](https://img.shields.io/badge/Version-1.1.7--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 2a0d731ad31d30234283a86dd8f2dd183b2d489c](https://img.shields.io/badge/AppVersion-2a0d731ad31d30234283a86dd8f2dd183b2d489c-informational?style=flat-square)
+![Version: 1.1.11-dev](https://img.shields.io/badge/Version-1.1.11--dev-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 2a0d731ad31d30234283a86dd8f2dd183b2d489c](https://img.shields.io/badge/AppVersion-2a0d731ad31d30234283a86dd8f2dd183b2d489c-informational?style=flat-square)
 
 A Helm chart for deploying the Seqr app, an open source software platform for rare disease genomics
 
@@ -21,7 +21,7 @@ A Helm chart for deploying the Seqr app, an open source software platform for ra
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../lib | lib | 0.1.3 |
+| file://../lib | lib | 0.1.4 |
 | https://charts.bitnami.com/bitnami | postgresql | 15.5.31 |
 | https://charts.bitnami.com/bitnami | redis | 19.0.2 |
 
@@ -129,7 +129,7 @@ false
 			<td>environment.HAIL_SEARCH_DATA_DIR</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr/seqr-hail-search-data"
+"/var/seqr/seqr-hail-search-data"
 </pre>
 </td>
 			<td></td>
@@ -138,7 +138,7 @@ false
 			<td>environment.LOADING_DATASETS_DIR</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr/seqr-loading-temp"
+"/var/seqr/seqr-loading-temp"
 </pre>
 </td>
 			<td></td>
@@ -219,7 +219,7 @@ false
 			<td>environment.STATIC_MEDIA_DIR</td>
 			<td>string</td>
 			<td><pre lang="json">
-null
+"/var/seqr/seqr-static-media"
 </pre>
 </td>
 			<td>If storing static media files in a local filesystem, the path to that filesystem</td>
@@ -257,6 +257,15 @@ null
 			<td><pre lang="json">
 false
 </pre>
+</td>
+			<td></td>
+		</tr>
+		<tr>
+			<td>initContainers</td>
+			<td>string</td>
+			<td><pre lang="json">
+"- name: mkdir-loading-datasets\n  image: busybox:1.35\n  imagePullPolicy: {{ $.Values.image.pullPolicy }}\n  command: ['/bin/mkdir', '-p', {{ $.Values.environment.LOADING_DATASETS_DIR }}]\n  {{- with $.Values.volumeMounts }}\n  volumeMounts:\n    {{- tpl . $ | nindent 4 }}\n  {{- end }}"
+</pre>
 </td>
 			<td></td>
 		</tr>
@@ -363,7 +372,7 @@ true
 			<td>postgresql.postgresqlDataDir</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr/postgresql-data"
+"/var/seqr/postgresql-data"
 </pre>
 </td>
 			<td></td>
@@ -462,7 +471,7 @@ false
 			<td>postgresql.primary.initContainers[0].volumeMounts[0].mountPath</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>
@@ -489,7 +498,7 @@ false
 			<td>postgresql.primary.persistence.mountPath</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>
@@ -643,18 +652,18 @@ true
 		</tr>
 		<tr>
 			<td>volumeMounts</td>
-			<td>object</td>
+			<td>string</td>
 			<td><pre lang="json">
-{}
+"- name: seqr-datasets\n  mountPath: /var/seqr\n  readOnly: false"
 </pre>
 </td>
 			<td></td>
 		</tr>
 		<tr>
 			<td>volumes</td>
-			<td>object</td>
+			<td>string</td>
 			<td><pre lang="json">
-{}
+"- name: seqr-datasets\n  persistentVolumeClaim:\n    readOnly: false\n    claimName: {{ include \"lib.pvc-name\" . }}"
 </pre>
 </td>
 			<td></td>
@@ -690,7 +699,7 @@ true
 			<td>lib.exports.global.lib.persistentVolume.local.path</td>
 			<td>string</td>
 			<td><pre lang="json">
-"/seqr"
+"/var/seqr"
 </pre>
 </td>
 			<td></td>