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Merged
LizBaldo merged 5 commits into from
Dec 6, 2024
Merged

Release Bioc 3.20 RStudio and Jupyter updates #497

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b9753df
Bump Bioconductor version
almahmoud Dec 4, 2024
6fb0528
Run ammonite versioning script
almahmoud Dec 4, 2024
66310c3
Update env variable with version
almahmoud Dec 4, 2024
d7d68e4
Update RStudio
almahmoud Dec 4, 2024
eaa4c56
small fixes
LizBaldo Dec 5, 2024
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22 changes: 11 additions & 11 deletions config/community_images.json
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Expand Up @@ -9,22 +9,22 @@
"isCommunity": true
},
{
"id": "RStudio",
"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",
"id": "Rstudio",
"label": "RStudio (R 4.4.2, Bioconductor 3.20, Python 3.12.3)",
"version": "3.20.0",
"updated": "2024-11-20",
"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.20.0-versions.json",
"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.0",
"requiresSpark": false,
"isRStudio": true
},
{
"id": "LegacyRStudio",
"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",
"label": "RStudio (R 4.4.1, Bioconductor 3.19, Python 3.10.12)",
"version": "3.19.1",
"updated": "2024-06-27",
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@lucymcnatt lucymcnatt Dec 6, 2024

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nit, shouldn't this be 11-20 as well?

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@LizBaldo LizBaldo Dec 6, 2024

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That is the legacy image though, not sure it needs updating

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@almahmoud almahmoud Dec 6, 2024

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I went by the date when the image was built. I don't think this is propagated to the UI though anyway, so it doesn't really matter

"packages": "https://raw.githubusercontent.com/anvilproject/anvil-docker/main/anvil-rstudio-bioconductor/info/anvil-rstudio-bioconductor-3.19.1-versions.json",
"image": "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.1",
"requiresSpark": false,
"isRStudio": true
}]
8 changes: 4 additions & 4 deletions config/conf.json
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Expand Up @@ -26,7 +26,7 @@
"tidyverse"
]
},
"version" : "2.2.5",
"version" : "2.2.6",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand Down Expand Up @@ -104,7 +104,7 @@
"packages" : {

},
"version" : "2.2.5",
"version" : "2.2.6",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : true,
Expand All @@ -124,7 +124,7 @@
"packages" : {

},
"version" : "2.3.7",
"version" : "2.3.8",
"automated_flags" : {
"include_in_ui" : true,
"generate_docs" : true,
Expand All @@ -143,7 +143,7 @@
"packages" : {

},
"version" : "2.2.13",
"version" : "2.2.14",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : false,
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7 changes: 7 additions & 0 deletions terra-jupyter-aou/CHANGELOG.md
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@@ -1,3 +1,10 @@
## 2.2.14 - 2024-12-04T17:30:49.302274524Z

- Update `terra-jupyter-r` to `2.2.6`
- Update for R 4.4.2 and Bioc 3.20

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14`

## 2.2.13 - 2024-08-12
- Update `hail` to `0.2.130.post1`
- See https://github.com/hail-is/hail/releases/tag/0.2.130.post1 for details
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10 changes: 5 additions & 5 deletions terra-jupyter-aou/Dockerfile
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@@ -1,4 +1,4 @@
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8

USER root

Expand Down Expand Up @@ -195,10 +195,10 @@ RUN apt-get update && \
&& rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && pip install --verbose h5py

# RW-8725 INSTALL QIMEE2
RUN curl -fsSL -o qiime2-2022.8.yml https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml && \
conda env create -n qiime2-2022.8 --file qiime2-2022.8.yml && \
rm qiime2-2022.8.yml
# QIIME 2 2024.5 Amplicon Distribution
RUN curl -fsSL -o qiime2-2024.5.yml https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml && \
conda env create -n qiime2-2024.5 --file qiime2-2024.5.yml && \
rm qiime2-2024.5.yml

# Install jellyfish
RUN mkdir -p /tmp/jellyfish && \
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7 changes: 7 additions & 0 deletions terra-jupyter-bioconductor/CHANGELOG.md
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## 2.2.6 - 2024-12-04T17:30:49.275803406Z

- Update `terra-jupyter-r` to `2.2.6`
- Update for R 4.4.2 and Bioc 3.20

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6`

## 2.2.5 - 2024-05-15T15:36:28.576892790Z

- Update `terra-jupyter-r` to `2.2.5`
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2 changes: 1 addition & 1 deletion terra-jupyter-bioconductor/Dockerfile
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@@ -1 +1 @@
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6
7 changes: 7 additions & 0 deletions terra-jupyter-gatk/CHANGELOG.md
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@@ -1,3 +1,10 @@
## 2.3.8 - 2024-12-04T17:30:49.287815033Z

- Update `terra-jupyter-r` to `2.2.6`
- Update for R 4.4.2 and Bioc 3.20

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8`

## 2.3.7 - 2024-05-15T15:36:28.602743427Z

- Update `terra-jupyter-r` to `2.2.5`
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6 changes: 4 additions & 2 deletions terra-jupyter-gatk/Dockerfile
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@@ -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:2.2.5
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6

USER root

Expand All @@ -27,7 +27,9 @@ ENV PIP_USER=false
# uninstalling packages: https://github.com/conda/conda/issues/10357
COPY --from=python /etc/terra-docker/requirements.txt /etc/terra-docker/base_requirements.txt

RUN pip install --upgrade -r /etc/terra-docker/base_requirements.txt
RUN pip install -r /etc/terra-docker/base_requirements.txt
# See: https://github.com/pypa/setuptools/issues/4483
RUN pip install "setuptools<71.0.0"

# Install GATK
ENV GATK_VERSION 4.3.0.0
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6 changes: 6 additions & 0 deletions terra-jupyter-r/CHANGELOG.md
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## 2.2.6 - 2024-12-04T17:30:49.258285293Z

- Update for R 4.4.2 and Bioc 3.20

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6`

## 2.2.5 - 2024-05-15T15:36:28.555690376Z

- Update for R 4.4.0 and Bioc 3.19
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6 changes: 3 additions & 3 deletions terra-jupyter-r/Dockerfile
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Expand Up @@ -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-2.2.5"
ENV TERRA_R_PLATFORM_BINARY_VERSION=3.19
ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.6"
ENV TERRA_R_PLATFORM_BINARY_VERSION=3.20

# 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 \
Expand Down Expand Up @@ -132,7 +132,7 @@ RUN pip3 -V \

RUN R -e 'install.packages("BiocManager")' \
## check version
&& R -e 'BiocManager::install(version="3.19", ask=FALSE)' \
&& R -e "BiocManager::install(version='$TERRA_R_PLATFORM_BINARY_VERSION', ask=FALSE)" \
&& R -e 'BiocManager::install(c( \
"boot", \
"class", \
Expand Down
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