Add changes from script

DataBiosphere · Nov 14, 2023 · 2582254 · 2582254
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commit 2582254
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Showing 9 changed files with 58 additions and 18 deletions.
diff --git a/config/conf.json b/config/conf.json
@@ -26,7 +26,7 @@
                     "tidyverse"
                 ]
             },
-            "version" : "2.2.3",
+            "version" : "2.2.4",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : true,
@@ -83,7 +83,9 @@
             "tools" : [
                 "python"
             ],
-            "packages" : {},
+            "packages" : {
+
+            },
             "version" : "1.1.3",
             "automated_flags" : {
                 "generate_docs" : true,
@@ -99,8 +101,10 @@
             "tools" : [
                 "r"
             ],
-            "packages" : {},
-            "version" : "2.2.3",
+            "packages" : {
+
+            },
+            "version" : "2.2.4",
             "automated_flags" : {
                 "include_in_ui" : false,
                 "generate_docs" : true,
@@ -117,8 +121,10 @@
                 "python",
                 "r"
             ],
-            "packages" : {},
-            "version" : "2.3.4",
+            "packages" : {
+
+            },
+            "version" : "2.3.5",
             "automated_flags" : {
                 "include_in_ui" : true,
                 "generate_docs" : true,
@@ -134,8 +140,10 @@
                 "python",
                 "r"
             ],
-            "packages" : {},
-            "version" : "2.2.7",
+            "packages" : {
+
+            },
+            "version" : "2.2.8",
             "automated_flags" : {
                 "include_in_ui" : false,
                 "generate_docs" : false,
@@ -150,7 +158,9 @@
             "tools" : [
                 "r"
             ],
-            "packages" : {},
+            "packages" : {
+
+            },
             "version" : "0.1.1",
             "automated_flags" : {
                 "include_in_ui" : false,
@@ -163,8 +173,11 @@
         {
             "name" : "wondershaper",
             "base_label" : "wondershaper",
-            "tools" : [],
-            "packages" : {},
+            "tools" : [
+            ],
+            "packages" : {
+
+            },
             "version" : "0.0.1",
             "automated_flags" : {
                 "include_in_ui" : false,
@@ -175,4 +188,4 @@
             }
         }
     ]
-}
+}
diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md
@@ -1,3 +1,10 @@
+## 2.2.8 - 2023-11-14T15:56:44.507726350Z
+
+- Update `terra-jupyter-r` to `1.1.4`
+  - Bioconductor 3.18 release
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.8`
+
 ## 2.2.7 - 2023-11-01
 - Pin `gnomad` to `0.6.4`
   - See https://github.com/broadinstitute/gnomad_methods/releases 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:2.3.4
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.5
 
 USER root
 

diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md
@@ -1,3 +1,10 @@
+## 2.2.4 - 2023-11-14T15:56:44.470211534Z
+
+- Update `terra-jupyter-r` to `1.1.4`
+  - Bioconductor 3.18 release
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.4`
+
 ## 2.2.3 - 2023-10-03
 - Update `terra-jupyter-r` to `2.2.3`
     - Update `terra-jupyter-base` to `1.1.3`

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:2.2.3
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.4
diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md
@@ -1,3 +1,10 @@
+## 2.3.5 - 2023-11-14T15:56:44.486168932Z
+
+- Update `terra-jupyter-r` to `1.1.4`
+  - Bioconductor 3.18 release
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.5`
+
 ## 2.3.4 - 2023-10-06
 - Update `terra-jupyter-python` to `1.1.4`
   - Downgrade pytz to `2023.3`

diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile
@@ -1,6 +1,6 @@
 FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4 AS python
 
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.3
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.4
 
 USER root
 

diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md
@@ -1,3 +1,9 @@
+## 1.1.4 - 2023-11-14T15:56:44.443656567Z
+
+- Bioconductor 3.18 release
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.1.4`
+
 ## 1.1.3 - 2023-10-03
 - Update `terra-jupyter-base` to `1.1.3`
    - Downgrade notebook to `6.5.4` and jupyterlab-server to `2.23.0`

diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile
@@ -5,8 +5,8 @@ USER root
 COPY scripts $JUPYTER_HOME/scripts
 
 # Add env vars to identify binary package installation
-ENV TERRA_R_PLATFORM="terra-jupyter-r-1.1.3"
-ENV TERRA_R_PLATFORM_BINARY_VERSION=3.17
+ENV TERRA_R_PLATFORM="terra-jupyter-r-1.1.4"
+ENV TERRA_R_PLATFORM_BINARY_VERSION=3.18
 
 # Install protobuf 3.20.3. Note this version comes from base deep learning image. Use `conda list` to see what's installed
 RUN cd /tmp \
@@ -128,7 +128,7 @@ RUN pip3 -V \
 
 RUN R -e 'install.packages("BiocManager")' \
     ## check version
-    && R -e 'BiocManager::install(version="3.17", ask=FALSE)' \
+    && R -e 'BiocManager::install(version="3.18", ask=FALSE)' \
     && R -e 'BiocManager::install(c( \
     "boot", \
     "class", \