diff --git a/charts/hail-search/README.md b/charts/hail-search/README.md
index bc758d9..d3f30ff 100644
--- a/charts/hail-search/README.md
+++ b/charts/hail-search/README.md
@@ -1,6 +1,6 @@
# hail-search
-  
+  
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
| environment.HAIL_SEARCH_DATA_DIR |
string |
-"/seqr/seqr-hail-search-data"
+"/var/seqr/seqr-hail-search-data"
|
|
@@ -71,7 +71,7 @@ false
environment.REFERENCE_DATASETS_DIR |
string |
-"/seqr/seqr-reference-data"
+"/var/seqr/seqr-reference-data"
|
|
@@ -197,7 +197,7 @@ true
volumeMounts |
string |
-"- name: seqr-datasets\n mountPath: /seqr\n readOnly: true"
+"- name: seqr-datasets\n mountPath: /var/seqr\n readOnly: true"
|
|
@@ -242,7 +242,7 @@ true
lib.exports.global.lib.persistentVolume.local.path |
string |
-"/seqr"
+"/var/seqr"
|
|
diff --git a/charts/lib/README.md b/charts/lib/README.md
index 1adb716..ec7a829 100644
--- a/charts/lib/README.md
+++ b/charts/lib/README.md
@@ -1,6 +1,6 @@
# lib
- 
+ 
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
exports.global.lib.persistentVolume.local.path |
string |
-"/seqr"
+"/var/seqr"
|
|
diff --git a/charts/pipeline-runner/README.md b/charts/pipeline-runner/README.md
index b0988af..4bf60a2 100644
--- a/charts/pipeline-runner/README.md
+++ b/charts/pipeline-runner/README.md
@@ -1,6 +1,6 @@
# pipeline-runner
-  
+  
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
pods[1].initContainers |
string |
-"- 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 }}"
|
|
@@ -368,7 +368,7 @@ true
volumeMounts |
string |
-"- name: seqr-datasets\n mountPath: /seqr\n readOnly: false"
+"- name: seqr-datasets\n mountPath: /var/seqr\n readOnly: false"
|
|
@@ -413,7 +413,7 @@ true
lib.exports.global.lib.persistentVolume.local.path |
string |
-"/seqr"
+"/var/seqr"
|
|
diff --git a/charts/seqr-platform/README.md b/charts/seqr-platform/README.md
index 9251159..8119973 100644
--- a/charts/seqr-platform/README.md
+++ b/charts/seqr-platform/README.md
@@ -1,6 +1,6 @@
# seqr-platform
- 
+ 
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
index a59bd27..d3a554e 100644
--- a/charts/seqr/README.md
+++ b/charts/seqr/README.md
@@ -1,6 +1,6 @@
# seqr
-  
+  
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
environment.HAIL_SEARCH_DATA_DIR |
string |
-"/seqr/seqr-hail-search-data"
+"/var/seqr/seqr-hail-search-data"
|
|
@@ -138,7 +138,7 @@ false
environment.LOADING_DATASETS_DIR |
string |
-"/seqr/seqr-loading-temp"
+"/var/seqr/seqr-loading-temp"
|
|
@@ -219,7 +219,7 @@ false
environment.STATIC_MEDIA_DIR |
string |
-null
+"/var/seqr/seqr-static-media"
|
If storing static media files in a local filesystem, the path to that filesystem |
@@ -257,6 +257,15 @@ null
false
+ |
+ |
+
+
+ | initContainers |
+ string |
+
+"- 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 }}"
+
|
|
@@ -363,7 +372,7 @@ true
postgresql.postgresqlDataDir |
string |
-"/seqr/postgresql-data"
+"/var/seqr/postgresql-data"
|
|
@@ -462,7 +471,7 @@ false
postgresql.primary.initContainers[0].volumeMounts[0].mountPath |
string |
-"/seqr"
+"/var/seqr"
|
|
@@ -489,7 +498,7 @@ false
postgresql.primary.persistence.mountPath |
string |
-"/seqr"
+"/var/seqr"
|
|
@@ -643,18 +652,18 @@ true
| volumeMounts |
- object |
+ string |
-{}
+"- name: seqr-datasets\n mountPath: /var/seqr\n readOnly: false"
|
|
| volumes |
- object |
+ string |
-{}
+"- name: seqr-datasets\n persistentVolumeClaim:\n readOnly: false\n claimName: {{ include \"lib.pvc-name\" . }}"
|
|
@@ -690,7 +699,7 @@ true
lib.exports.global.lib.persistentVolume.local.path |
string |
-"/seqr"
+"/var/seqr"
|
|