From 75a6e60700ba104626e9d49edf0fcf712720463c Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Thu, 16 May 2024 16:44:24 -0400 Subject: [PATCH] Update Jupyter and RStudio for 3.19 release (#488) * Update for 3.19 * Ammonite script run * we should not need to reinstall nbconvert * reinstall both nbconvert and dateutil * need to force reinstall dateutils first * adding the --no-deps flag * using --ignore-installed instead seems to work locally * pin nbconvert to the latest working version currently in prod --------- Co-authored-by: LizBaldo --- config/community_images.json | 20 ++++++------- config/conf.json | 37 +++++++++++++++++-------- terra-jupyter-aou/CHANGELOG.md | 7 +++++ terra-jupyter-aou/Dockerfile | 2 +- terra-jupyter-bioconductor/CHANGELOG.md | 7 +++++ terra-jupyter-bioconductor/Dockerfile | 2 +- terra-jupyter-gatk/CHANGELOG.md | 7 +++++ terra-jupyter-gatk/Dockerfile | 9 +++--- terra-jupyter-r/CHANGELOG.md | 6 ++++ terra-jupyter-r/Dockerfile | 6 ++-- 10 files changed, 71 insertions(+), 32 deletions(-) diff --git a/config/community_images.json b/config/community_images.json index 8c322c4b..dec92e03 100644 --- a/config/community_images.json +++ b/config/community_images.json @@ -10,21 +10,21 @@ }, { "id": "RStudio", - "label": "RStudio (R 4.3.2, Bioconductor 3.18, Python 3.10.12)", - "version": "3.18.0", - "updated": "2023-11-07", - "packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.18.0-versions.json", - "image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.18.0", + "label": "RStudio (R 4.4.0, Bioconductor 3.19, Python 3.10.12)", + "version": "3.19.0", + "updated": "2024-05-13", + "packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.19.0-versions.json", + "image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0", "requiresSpark": false, "isRStudio": true }, { "id": "LegacyRStudio", - "label": "RStudio (R 4.3.1, Bioconductor 3.17, Python 3.10.12)", - "version": "3.17.1", - "updated": "2023-09-13", - "packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.17.1-versions.json", - "image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.17.1", + "label": "RStudio (R 4.3.3, Bioconductor 3.18, Python 3.10.12)", + "version": "3.18.1", + "updated": "2024-05-13", + "packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.18.1-versions.json", + "image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.18.1", "requiresSpark": false, "isRStudio": true }] diff --git a/config/conf.json b/config/conf.json index feab6658..5b6afdc7 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.2.4", + "version" : "2.2.5", "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" : "2.2.4", + "packages" : { + + }, + "version" : "2.2.5", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -117,8 +121,10 @@ "python", "r" ], - "packages" : {}, - "version" : "2.3.6", + "packages" : { + + }, + "version" : "2.3.7", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -134,8 +140,10 @@ "python", "r" ], - "packages" : {}, - "version" : "2.2.11", + "packages" : { + + }, + "version" : "2.2.12", "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 4cd8e38a..e83d1a36 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.2.12 - 2024-05-15T15:36:28.616710060Z + +- Update `terra-jupyter-r` to `2.2.5` + - Update for R 4.4.0 and Bioc 3.19 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.12` + ## 2.2.11 - 2024-04-10 - Update `hail` to `0.2.130` - See https://hail.is/docs/0.2/change_log.html#version-0-2-130) for details diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index 8795c4a7..27fdd6f5 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:2.3.6 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7 USER root diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 81b065c6..dce91612 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.2.5 - 2024-05-15T15:36:28.576892790Z + +- Update `terra-jupyter-r` to `2.2.5` + - Update for R 4.4.0 and Bioc 3.19 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.5` + ## 2.2.4 - 2023-11-14T15:56:44.470211534Z - Update `terra-jupyter-r` to `2.2.4` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index 6c464213..916163fd 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1 +1 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.4 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5 diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 1161275d..0069b6df 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.3.7 - 2024-05-15T15:36:28.602743427Z + +- Update `terra-jupyter-r` to `2.2.5` + - Update for R 4.4.0 and Bioc 3.19 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7` + ## 2.3.6 - 2023-11-27 - Update Samtools to `1.18` diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index b63bbb4a..4e182a70 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:1.1.5 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.4 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5 USER root @@ -90,8 +90,9 @@ COPY cnn-models.patch /etc/gatk-$GATK_VERSION/cnn-models.patch RUN patch -u /opt/conda/lib/python3.10/site-packages/vqsr_cnn/vqsr_cnn/models.py -i /etc/gatk-$GATK_VERSION/cnn-models.patch -# Older version of nbconvert fail to convert notebooks to html -RUN pip3 install "nbconvert>=7.7.3" +# Newer version of nbconvert fail to convert notebooks to html +RUN pip3 install --ignore-installed python-dateutil==2.8.2 \ + && pip3 install "nbconvert==7.11.0" ENV PIP_USER=true @@ -99,5 +100,3 @@ ENV PIP_USER=true ENV USER jupyter USER $USER - - diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index c271fb66..6a369f7a 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.2.5 - 2024-05-15T15:36:28.555690376Z + +- Update for R 4.4.0 and Bioc 3.19 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5` + ## 2.2.4 - 2023-11-14T15:56:44.443656567Z - Bioconductor 3.18 release diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 173ede78..985b154b 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-2.2.4" -ENV TERRA_R_PLATFORM_BINARY_VERSION=3.18 +ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.5" +ENV TERRA_R_PLATFORM_BINARY_VERSION=3.19 # 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 \ @@ -132,7 +132,7 @@ RUN pip3 -V \ RUN R -e 'install.packages("BiocManager")' \ ## check version - && R -e 'BiocManager::install(version="3.18", ask=FALSE)' \ + && R -e 'BiocManager::install(version="3.19", ask=FALSE)' \ && R -e 'BiocManager::install(c( \ "boot", \ "class", \