From 4ea5657d3b859280a226b6cc2004d1086c5da55b Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 9 Oct 2024 08:09:44 -0400 Subject: [PATCH] Bump docs --- charts/hail-search/README.md | 12 +++++------ charts/lib/README.md | 4 ++-- charts/pipeline-runner/README.md | 10 ++++----- charts/seqr-platform/README.md | 10 ++++----- charts/seqr/README.md | 35 ++++++++++++++++++++------------ 5 files changed, 40 insertions(+), 31 deletions(-) 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 -![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 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 -![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 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 -![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 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 -![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 index a59bd27..d3a554e 100644 --- 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 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"