diff --git a/config/conf.json b/config/conf.json index 5753adf5..23acec05 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.1.10", + "version" : "2.1.11", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.1.9", + "version" : "2.1.10", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.2.12", + "version" : "2.2.13", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.1.21", + "version" : "2.1.22", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, @@ -181,7 +181,7 @@ "packages" : { }, - "version" : "0.2.9", + "version" : "0.2.10", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, diff --git a/config/legacy_static_images.json b/config/legacy_static_images.json index 7e0c1434..5cd1a167 100644 --- a/config/legacy_static_images.json +++ b/config/legacy_static_images.json @@ -1,11 +1,11 @@ [ { - "updated": "2022-11-15", - "image": "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.1.7", - "label": "Legacy R / Bioconductor (R 4.1.2, Bioconductor 3.15, Python 3.7.12)", - "version": "2.1.7", + "updated": "2023-02-09", + "image": "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.1.9", + "label": "Legacy R / Bioconductor (R 4.2.2, Bioconductor 3.16, Python 3.7.12)", + "version": "2.1.9", "requiresSpark": false, - "packages": "https://storage.googleapis.com/terra-docker-image-documentation/terra-jupyter-bioconductor-2.1.7-versions.json", + "packages": "https://storage.googleapis.com/terra-docker-image-documentation/terra-jupyter-bioconductor-2.1.9-versions.json", "id": "terra-jupyter-bioconductor_legacy" } ] diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index 6874e25e..7709ec23 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.1.22 - 2023-06-01T17:49:47.721962740Z + +- Update `terra-jupyter-r` to `2.1.10` + - Bioconductor 3.17 release with R 4.3 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.1.22` + ## 2.1.21 - 2023-05-24 - Rollback `hail` to `0.2.107` - Fix `cromshell` alias typo diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index e2767d17..a3bec54b 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:2.2.11 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.12 USER root diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 7deceb1d..f4a06047 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.1.11 - 2023-06-01T17:49:47.622531112Z + +- Update `terra-jupyter-r` to `2.1.10` + - Bioconductor 3.17 release with R 4.3 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.1.11` + ## 2.1.10 - 2023-03-13T17:26:34.148443Z - Update `terra-jupyter-base` to `1.0.14` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index e91ee26c..4bc5e08d 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1 +1 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.9 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index f7c11d09..bb7394fa 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,3 +1,10 @@ +## 0.2.10 - 2023-06-01T17:49:47.736670188Z + +- Update `terra-jupyter-r` to `2.1.10` + - Bioconductor 3.17 release with R 4.3 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.2.10` + ## 0.2.9 - 2023-03-13T17:26:34.258214Z - Update `terra-jupyter-base` to `1.0.14` diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index a8aa759f..6b820ec1 100644 --- a/terra-jupyter-gatk-ovtf/Dockerfile +++ b/terra-jupyter-gatk-ovtf/Dockerfile @@ -1,6 +1,6 @@ FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.13 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.9 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 # copy everything pip installed from the python image COPY --from=python /opt/conda/lib/python3.7/site-packages /opt/conda/lib/python3.7/site-packages diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 388b50f1..df05706f 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.2.13 - 2023-06-01T17:49:47.668283846Z + +- Update `terra-jupyter-r` to `2.1.10` + - Bioconductor 3.17 release with R 4.3 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.13` + ## 2.2.12 - 2023-05-31T13:55:05 - Add bcftools diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 4da89c2d..86633cea 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:1.0.15 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.9 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 USER root diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index 07111802..c12d23cd 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.1.10 - 2023-06-01T17:49:47.585402026Z + +- Bioconductor 3.17 release with R 4.3 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10` + ## 2.1.9 - 2023-03-13T17:26:34.207471Z - Update `terra-jupyter-base` to `1.0.14` diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index fd6a9b3a..cdb5f208 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -5,7 +5,7 @@ COPY scripts $JUPYTER_HOME/scripts # Add env vars to identify binary package installation ENV TERRA_R_PLATFORM="terra-jupyter-r" -ENV TERRA_R_PLATFORM_BINARY_VERSION=3.16.0 +ENV TERRA_R_PLATFORM_BINARY_VERSION=3.17 # Install protobuf 3.19.1. Note this version comes from base deep learning image. Use `conda list` to see what's installed RUN cd /tmp \ @@ -96,6 +96,12 @@ RUN apt-get update \ libzmq3-dev \ libsbml5-dev \ biber \ + ## for gpuMagic package + ocl-icd-opencl-dev \ + ## for ChemmineOB package + libeigen3-dev \ + ## for rawrr package + mono-runtime \ && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.so /usr/lib/x86_64-linux-gnu/libgfortran.so \ && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libstdc++.so /usr/lib/x86_64-linux-gnu/libstdc++.so \ && apt-get clean \ @@ -121,7 +127,7 @@ RUN pip3 -V \ RUN R -e 'install.packages("BiocManager")' \ ## check version - && R -e 'BiocManager::install(version="3.16", ask=FALSE)' \ + && R -e 'BiocManager::install(version="3.17", ask=FALSE)' \ && R -e 'BiocManager::install(c( \ "boot", \ "class", \