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LizBaldo
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Release Bioc 3.20 RStudio and Jupyter updates (#497)
* Bump Bioconductor version * Run ammonite versioning script * Update env variable with version * Update RStudio * small fixes --------- Co-authored-by: LizBaldo <[email protected]>
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‎config/community_images.json‎

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"isCommunity": true
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},
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{
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"id": "RStudio",
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"label": "RStudio (R 4.4.0, Bioconductor 3.19, Python 3.10.12)",
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"version": "3.19.0",
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"updated": "2024-05-13",
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"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.19.0-versions.json",
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"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0",
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"id": "Rstudio",
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"label": "RStudio (R 4.4.2, Bioconductor 3.20, Python 3.12.3)",
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"version": "3.20.0",
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"updated": "2024-11-20",
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"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.20.0-versions.json",
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"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.0",
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"requiresSpark": false,
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"isRStudio": true
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},
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{
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"id": "LegacyRStudio",
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"label": "RStudio (R 4.3.3, Bioconductor 3.18, Python 3.10.12)",
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"version": "3.18.1",
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"updated": "2024-05-13",
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"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.18.1-versions.json",
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"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.18.1",
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"label": "RStudio (R 4.4.1, Bioconductor 3.19, Python 3.10.12)",
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"version": "3.19.1",
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"updated": "2024-06-27",
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"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.19.1-versions.json",
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"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.1",
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"requiresSpark": false,
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"isRStudio": true
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}]

‎config/conf.json‎

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"tidyverse"
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]
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},
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"version" : "2.2.5",
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"version" : "2.2.6",
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"automated_flags" : {
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"generate_docs" : true,
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"include_in_ui" : true,
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"packages" : {
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},
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"version" : "2.2.5",
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"version" : "2.2.6",
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"automated_flags" : {
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"include_in_ui" : false,
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"generate_docs" : true,
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"packages" : {
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},
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"version" : "2.3.7",
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"version" : "2.3.8",
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"automated_flags" : {
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"include_in_ui" : true,
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"generate_docs" : true,
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"packages" : {
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},
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"version" : "2.2.13",
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"version" : "2.2.14",
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"automated_flags" : {
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"include_in_ui" : false,
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"generate_docs" : false,

‎terra-jupyter-aou/CHANGELOG.md‎

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## 2.2.14 - 2024-12-04T17:30:49.302274524Z
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- Update `terra-jupyter-r` to `2.2.6`
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- Update for R 4.4.2 and Bioc 3.20
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Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14`
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## 2.2.13 - 2024-08-12
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- Update `hail` to `0.2.130.post1`
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- See https://github.com/hail-is/hail/releases/tag/0.2.130.post1 for details

‎terra-jupyter-aou/Dockerfile‎

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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7
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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8
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USER root
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&& rm -rf /var/lib/apt/lists/*
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RUN pip install --upgrade pip && pip install --verbose h5py
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# RW-8725 INSTALL QIMEE2
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RUN curl -fsSL -o qiime2-2022.8.yml https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml && \
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conda env create -n qiime2-2022.8 --file qiime2-2022.8.yml && \
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rm qiime2-2022.8.yml
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# QIIME 2 2024.5 Amplicon Distribution
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RUN curl -fsSL -o qiime2-2024.5.yml https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml && \
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conda env create -n qiime2-2024.5 --file qiime2-2024.5.yml && \
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rm qiime2-2024.5.yml
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# Install jellyfish
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RUN mkdir -p /tmp/jellyfish && \

‎terra-jupyter-bioconductor/CHANGELOG.md‎

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## 2.2.6 - 2024-12-04T17:30:49.275803406Z
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- Update `terra-jupyter-r` to `2.2.6`
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- Update for R 4.4.2 and Bioc 3.20
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Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6`
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## 2.2.5 - 2024-05-15T15:36:28.576892790Z
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- Update `terra-jupyter-r` to `2.2.5`

‎terra-jupyter-bioconductor/Dockerfile‎

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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6

‎terra-jupyter-gatk/CHANGELOG.md‎

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## 2.3.8 - 2024-12-04T17:30:49.287815033Z
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- Update `terra-jupyter-r` to `2.2.6`
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- Update for R 4.4.2 and Bioc 3.20
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Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8`
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## 2.3.7 - 2024-05-15T15:36:28.602743427Z
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- Update `terra-jupyter-r` to `2.2.5`

‎terra-jupyter-gatk/Dockerfile‎

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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5 AS python
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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6
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# uninstalling packages: https://github.com/conda/conda/issues/10357
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COPY --from=python /etc/terra-docker/requirements.txt /etc/terra-docker/base_requirements.txt
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RUN pip install --upgrade -r /etc/terra-docker/base_requirements.txt
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RUN pip install -r /etc/terra-docker/base_requirements.txt
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# See: https://github.com/pypa/setuptools/issues/4483
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RUN pip install "setuptools<71.0.0"
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# Install GATK
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ENV GATK_VERSION 4.3.0.0

‎terra-jupyter-r/CHANGELOG.md‎

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## 2.2.6 - 2024-12-04T17:30:49.258285293Z
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- Update for R 4.4.2 and Bioc 3.20
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Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6`
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## 2.2.5 - 2024-05-15T15:36:28.555690376Z
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- Update for R 4.4.0 and Bioc 3.19

‎terra-jupyter-r/Dockerfile‎

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COPY scripts $JUPYTER_HOME/scripts
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# Add env vars to identify binary package installation
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ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.5"
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ENV TERRA_R_PLATFORM_BINARY_VERSION=3.19
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ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.6"
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ENV TERRA_R_PLATFORM_BINARY_VERSION=3.20
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# Install protobuf 3.20.3. Note this version comes from base deep learning image. Use `conda list` to see what's installed
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## check version
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&& R -e 'BiocManager::install(version="3.19", ask=FALSE)' \
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&& R -e "BiocManager::install(version='$TERRA_R_PLATFORM_BINARY_VERSION', ask=FALSE)" \
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&& R -e 'BiocManager::install(c( \
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"boot", \
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"class", \

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