DataBiosphere · LizBaldo · Sep 18, 2024 · Sep 3, 2024 · Sep 4, 2024 · Sep 5, 2024
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -6,7 +6,7 @@
 
 We do our work on a feature branch based on master. When you open a pull request, add the JIRA issue number to the PR title. This will make a reference from JIRA to the GitHub issue. Briefly describe your changes in the description section.
 
-This is also a good opportunity to verify that all the appropriate image versions were bumped. It is important to keep in mind which images extend from where ([Image Dependecies](https://github.com/DataBiosphere/terra-docker#image-dependencies)). Make sure to bump the version of the image you are changing and update its reference in all images that extend from it.
+This is also a good opportunity to verify that all the appropriate image versions were bumped. It is important to keep in mind which images extend from where ([Image Dependecies](https://github.com/DataBiosphere/terra-docker#image-dependencies)). Make sure to bump the version of the image you are changing in `config/conf.json` and update its reference in all images that extend from it.
 
 You can also run `amm ./updateVersions.sc <image name> <release note>` to upgrade derived images. If you're updating `terra-jupyter-aou` image, please make a pull request similar to [this PR](https://github.com/DataBiosphere/leonardo/pull/1612) (less updating `terra_jupyter_aou_old`).
 

diff --git a/config/conf.json b/config/conf.json
@@ -26,7 +26,7 @@
                     "tidyverse"
                 ]
             },
-            "version" : "2.2.5",
+            "version" : "2.2.6",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : true,
@@ -47,7 +47,7 @@
                     "hail"
                 ]
             },
-            "version" : "1.1.12",
+            "version" : "1.1.13",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : true,
@@ -68,7 +68,7 @@
                     "scikit-learn"
                 ]
             },
-            "version" : "1.1.5",
+            "version" : "1.1.6",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : true,
@@ -84,9 +84,9 @@
                 "python"
             ],
             "packages" : {
-                
+
             },
-            "version" : "1.1.3",
+            "version" : "1.1.4",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : false,
@@ -102,9 +102,9 @@
                 "r"
             ],
             "packages" : {
-                
+
             },
-            "version" : "2.2.5",
+            "version" : "2.2.6",
             "automated_flags" : {
                 "include_in_ui" : false,
                 "generate_docs" : true,
@@ -122,9 +122,9 @@
                 "r"
             ],
             "packages" : {
-                
+
             },
-            "version" : "2.3.7",
+            "version" : "2.3.8",
             "automated_flags" : {
                 "include_in_ui" : true,
                 "generate_docs" : true,
@@ -141,9 +141,9 @@
                 "r"
             ],
             "packages" : {
-                
+
             },
-            "version" : "2.2.13",
+            "version" : "2.2.14",
             "automated_flags" : {
                 "include_in_ui" : false,
                 "generate_docs" : false,
@@ -159,7 +159,7 @@
                 "r"
             ],
             "packages" : {
-                
+
             },
             "version" : "0.1.1",
             "automated_flags" : {
@@ -176,7 +176,7 @@
             "tools" : [
             ],
             "packages" : {
-                
+
             },
             "version" : "0.0.1",
             "automated_flags" : {

diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 2.2.14 - 2024-09-04
+- Update `terra-jupyter-gatk` to `2.3.8`
+  - Update `terra-jupyter-python` to `1.1.6`
+    - Update `terra-jupyter-base` to `1.1.4`
+      - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14`
+
 ## 2.2.13 - 2024-08-12
 - Update `hail` to `0.2.130.post1`
   - See https://github.com/hail-is/hail/releases/tag/0.2.130.post1 for details

diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8
 
 USER root
 

diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md
@@ -1,3 +1,8 @@
+## 1.1.4 - 2024-09-04
+- Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.4`
+
 ## 1.1.3 - 2023-10-03
 - Downgrade notebook to `6.5.4` and jupyterlab-server to `2.23.0`
 

diff --git a/terra-jupyter-base/Dockerfile b/terra-jupyter-base/Dockerfile
@@ -111,7 +111,7 @@ RUN pip3 -V \
     && pip3 install jupyterlab-server==2.23.0 \
     && pip3 install requests \
     && pip3 install firecloud \
-    && pip3 install terra-notebook-utils==0.13.0 \
+    && pip3 install terra-notebook-utils==0.14.0 \
     && pip3 install crcmod \
     # For gcloud alpha storage support.
     && pip3 install google-crc32c --target /usr/lib/google-cloud-sdk/lib/third_party \

diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 2.2.6 - 2024-09-04
+
+- Update `terra-jupyter-r` to `2.2.6`
+  - Update `terra-jupyter-base` to `1.1.4`
+    - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6`
+
 ## 2.2.5 - 2024-05-15T15:36:28.576892790Z
 
 - Update `terra-jupyter-r` to `2.2.5`

diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile
@@ -1 +1 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6
diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md
@@ -1,3 +1,10 @@
+## 2.3.8 - 2024-09-04
+- Update `terra-jupyter-python` to `1.1.6`
+  - Update `terra-jupyter-base` to `1.1.4`
+    - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8`
+
 ## 2.3.7 - 2024-05-15T15:36:28.602743427Z
 
 - Update `terra-jupyter-r` to `2.2.5`

diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5 AS python
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.6 AS python
 
 FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
 

diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md
@@ -1,3 +1,10 @@
+## 1.1.13 - 2024-09-04
+- Update `terra-jupyter-python` to `1.1.6`
+  - Update `terra-jupyter-base` to `1.1.4`
+    - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.13`
+
 ## 1.1.12 - 2024-08-12
 - Update `hail` to `0.2.130.post1`
   - See https://github.com/hail-is/hail/releases/tag/0.2.130.post1 for details

diff --git a/terra-jupyter-hail/Dockerfile b/terra-jupyter-hail/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.6
 
 USER root
 

diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md
@@ -1,3 +1,9 @@
+## 1.1.6 - 2024-09-04
+- Update `terra-jupyter-base` to `1.1.4`
+  - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.6`
+
 ## 1.1.5 - 2023-11-28
 - Pin bleach to `6.0.0`
 

diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.4
 
 USER root
 # This makes it so pip runs as root, not the user.

diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md
@@ -1,3 +1,9 @@
+## 2.2.6 - 2024-09-04
+- Update `terra-jupyter-base` to `1.1.4`
+  - Update terra-notebook-utils to `0.14.0`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6`
+
 ## 2.2.5 - 2024-05-15T15:36:28.555690376Z
 
 - Update for R 4.4.0 and Bioc 3.19

diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.4
 
 USER root
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
		FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6