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Update main from release-2025.05.01 #466

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0ee4775
new builds
hhuuggoo Dec 16, 2025
00ff937
fix miniconda
hhuuggoo Dec 17, 2025
97c1bfa
handle amd
hhuuggoo Dec 17, 2025
8afc451
no more mamba
hhuuggoo Dec 17, 2025
9a40a8e
bump sqlite
hhuuggoo Dec 18, 2025
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2 changes: 1 addition & 1 deletion common/install-jupyter.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions common/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions common/jupyter-environment.yml
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Expand Up @@ -19,6 +19,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 2 additions & 0 deletions common/jupyter-gpu-environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturn-python-312-slim-gpu-12.9/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ ARG SATURNBASE_GPU_IMAGE
FROM ${SATURNBASE_GPU_IMAGE}

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-python-312-slim/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ ARG SATURNBASE_IMAGE
FROM ${SATURNBASE_IMAGE}

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
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2 changes: 1 addition & 1 deletion saturn-python-llm/Dockerfile
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Expand Up @@ -6,7 +6,7 @@ RUN sudo apt-get -qq --allow-releaseinfo-change update && \
libgl1

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-python-pytorch/Dockerfile
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Expand Up @@ -6,7 +6,7 @@ RUN sudo apt-get -qq --allow-releaseinfo-change update && \
libgl1

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-python-rapids/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ ARG SATURNBASE_GPU_IMAGE
FROM ${SATURNBASE_GPU_IMAGE}

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-python-tensorflow/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ ARG SATURNBASE_GPU_IMAGE
FROM ${SATURNBASE_GPU_IMAGE}

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-python/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ ARG SATURNBASE_IMAGE
FROM ${SATURNBASE_IMAGE}

COPY environment.yml /tmp/environment.yml
RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
${CONDA_DIR}/envs/saturn/bin/python -m ipykernel install \
--name python3 \
--display-name 'saturn (Python 3)' \
Expand Down
2 changes: 1 addition & 1 deletion saturn-r-bioconductor/Dockerfile
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Expand Up @@ -5,7 +5,7 @@ FROM ${SATURNBASE_IMAGE}
COPY environment.yml /tmp/environment.yml
COPY postBuild /tmp/postBuild.sh

RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
find ${CONDA_DIR} -type f,l -name '*.pyc' -delete && \
find ${CONDA_DIR} -type f,l -name '*.a' -delete && \
find ${CONDA_DIR} -type f,l -name '*.js.map' -delete && \
Expand Down
2 changes: 1 addition & 1 deletion saturn-r/Dockerfile
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Expand Up @@ -5,7 +5,7 @@ FROM ${SATURNBASE_IMAGE}
COPY environment.yml /tmp/environment.yml
COPY postBuild /tmp/postBuild.sh

RUN mamba env update -n saturn --file /tmp/environment.yml && \
RUN conda env update -n saturn --file /tmp/environment.yml && \
find ${CONDA_DIR} -type f,l -name '*.pyc' -delete && \
find ${CONDA_DIR} -type f,l -name '*.a' -delete && \
find ${CONDA_DIR} -type f,l -name '*.js.map' -delete && \
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-amd-gpu-devel/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-amd-gpu-devel/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-11.8/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-11.8/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-11.8/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-12.1/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-12.1/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-12.1/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-12.9/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-12.9/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-12.9/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-devel-11.8/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-devel-11.8/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-devel-11.8/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-devel-12.1/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-devel-12.1/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-devel-12.1/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
2 changes: 2 additions & 0 deletions saturnbase-python-gpu-devel-12.9/environment.yml
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Expand Up @@ -20,6 +20,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python-gpu-devel-12.9/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python-gpu-devel-12.9/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
1 change: 0 additions & 1 deletion saturnbase-python/Makefile
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Expand Up @@ -3,7 +3,6 @@ export

build_image:
docker build \
--no-cache \
--build-arg JUPYTER_SATURN_VERSION=${JUPYTER_SATURN_VERSION} \
-t ${IMAGE} \
.
2 changes: 2 additions & 0 deletions saturnbase-python/environment.yml
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Expand Up @@ -19,6 +19,8 @@ dependencies:
- tornado
- voila
- yarl
- sqlite=3.51.1
- libsqlite=3.51.1
- pip:
- jupyter_server
- jupyter_bokeh
Expand Down
2 changes: 1 addition & 1 deletion saturnbase-python/install-jupyter.bash
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Expand Up @@ -7,7 +7,7 @@ cd $(dirname $0)

echo "installing root env:"
cat /tmp/environment.yml
mamba env update -n base -f /tmp/environment.yml
conda env update -n base -f /tmp/environment.yml
conda clean -afy
jupyter lab clean
find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
Expand Down
4 changes: 2 additions & 2 deletions saturnbase-python/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
4 changes: 2 additions & 2 deletions saturnbase-r-bioconductor/.env_deps
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@@ -1,2 +1,2 @@
VERSION=2022.06.01
IMAGE=public.ecr.aws/saturncloud/saturnbase-r-bioconductor:2022.06.01.dev
VERSION=2025.12.01
IMAGE=public.ecr.aws/saturncloud/saturnbase-r-bioconductor:2025.12.01
2 changes: 1 addition & 1 deletion saturnbase-r-bioconductor/Dockerfile
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@@ -1,4 +1,4 @@
FROM bioconductor/bioconductor_docker:RELEASE_3_21
FROM bioconductor/bioconductor_docker:RELEASE_3_22
RUN usermod -l jovyan rstudio && \
groupmod -n jovyan rstudio && \
usermod -d /home/jovyan jovyan && \
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4 changes: 2 additions & 2 deletions saturnbase-r-bioconductor/install-miniconda.bash
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Expand Up @@ -10,9 +10,9 @@ set -x && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/saturncloud && \
rm miniconda.sh shasum && \
/opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes
/opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \
ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \
find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \
/opt/saturncloud/bin/conda clean -afy && \
chown -R 1000:1000 /opt/saturncloud
chown -R 1000:1000 /opt/saturncloud
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