diff --git a/config/conf.json b/config/conf.json index 3a94813c..fbb80b59 100644 --- 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 @@ } } ] -} +} \ No newline at end of file diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index f3297f41..50b063c5 100644 --- 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 index 7d16839a..bd2f3a76 100644 --- 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 index 3f583f0f..e69a8e6a 100644 --- 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 index 13b2004e..6c464213 100644 --- 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 index a9d3b301..ee46e6ec 100644 --- 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 index ba3158e4..e8a2eca9 100644 --- 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 index 2186b5e8..e9c0f1f9 100644 --- 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 index c18299a3..0cdc19f1 100644 --- 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", \