diff --git a/common/install-jupyter.bash b/common/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/common/install-jupyter.bash +++ b/common/install-jupyter.bash @@ -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 diff --git a/common/install-miniconda.bash b/common/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/common/install-miniconda.bash +++ b/common/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/common/jupyter-environment.yml b/common/jupyter-environment.yml index b315e38..75ce0ee 100644 --- a/common/jupyter-environment.yml +++ b/common/jupyter-environment.yml @@ -19,6 +19,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/common/jupyter-gpu-environment.yml b/common/jupyter-gpu-environment.yml index 0302ba9..a3755a8 100644 --- a/common/jupyter-gpu-environment.yml +++ b/common/jupyter-gpu-environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturn-python-312-slim-gpu-12.9/Dockerfile b/saturn-python-312-slim-gpu-12.9/Dockerfile index 9998724..9aecd52 100644 --- a/saturn-python-312-slim-gpu-12.9/Dockerfile +++ b/saturn-python-312-slim-gpu-12.9/Dockerfile @@ -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)' \ diff --git a/saturn-python-312-slim/Dockerfile b/saturn-python-312-slim/Dockerfile index 14e7a2d..f8900aa 100644 --- a/saturn-python-312-slim/Dockerfile +++ b/saturn-python-312-slim/Dockerfile @@ -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)' \ diff --git a/saturn-python-llm/Dockerfile b/saturn-python-llm/Dockerfile index 6fb0d73..993ed55 100644 --- a/saturn-python-llm/Dockerfile +++ b/saturn-python-llm/Dockerfile @@ -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)' \ diff --git a/saturn-python-pytorch/Dockerfile b/saturn-python-pytorch/Dockerfile index 6fb0d73..993ed55 100644 --- a/saturn-python-pytorch/Dockerfile +++ b/saturn-python-pytorch/Dockerfile @@ -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)' \ diff --git a/saturn-python-rapids/Dockerfile b/saturn-python-rapids/Dockerfile index 0d2d111..15d9216 100644 --- a/saturn-python-rapids/Dockerfile +++ b/saturn-python-rapids/Dockerfile @@ -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)' \ diff --git a/saturn-python-tensorflow/Dockerfile b/saturn-python-tensorflow/Dockerfile index 8ada0f9..70b5f1d 100644 --- a/saturn-python-tensorflow/Dockerfile +++ b/saturn-python-tensorflow/Dockerfile @@ -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)' \ diff --git a/saturn-python/Dockerfile b/saturn-python/Dockerfile index f2b2536..275c5dc 100644 --- a/saturn-python/Dockerfile +++ b/saturn-python/Dockerfile @@ -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)' \ diff --git a/saturn-r-bioconductor/Dockerfile b/saturn-r-bioconductor/Dockerfile index 37a4c84..f255f6c 100644 --- a/saturn-r-bioconductor/Dockerfile +++ b/saturn-r-bioconductor/Dockerfile @@ -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 && \ diff --git a/saturn-r/Dockerfile b/saturn-r/Dockerfile index 37a4c84..f255f6c 100644 --- a/saturn-r/Dockerfile +++ b/saturn-r/Dockerfile @@ -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 && \ diff --git a/saturnbase-python-amd-gpu-devel/install-jupyter.bash b/saturnbase-python-amd-gpu-devel/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-amd-gpu-devel/install-jupyter.bash +++ b/saturnbase-python-amd-gpu-devel/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-amd-gpu-devel/install-miniconda.bash b/saturnbase-python-amd-gpu-devel/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-amd-gpu-devel/install-miniconda.bash +++ b/saturnbase-python-amd-gpu-devel/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-11.8/environment.yml b/saturnbase-python-gpu-11.8/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-11.8/environment.yml +++ b/saturnbase-python-gpu-11.8/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-11.8/install-jupyter.bash b/saturnbase-python-gpu-11.8/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-11.8/install-jupyter.bash +++ b/saturnbase-python-gpu-11.8/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-gpu-11.8/install-miniconda.bash b/saturnbase-python-gpu-11.8/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-11.8/install-miniconda.bash +++ b/saturnbase-python-gpu-11.8/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-12.1/environment.yml b/saturnbase-python-gpu-12.1/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-12.1/environment.yml +++ b/saturnbase-python-gpu-12.1/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-12.1/install-jupyter.bash b/saturnbase-python-gpu-12.1/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-12.1/install-jupyter.bash +++ b/saturnbase-python-gpu-12.1/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-gpu-12.1/install-miniconda.bash b/saturnbase-python-gpu-12.1/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-12.1/install-miniconda.bash +++ b/saturnbase-python-gpu-12.1/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-12.9/environment.yml b/saturnbase-python-gpu-12.9/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-12.9/environment.yml +++ b/saturnbase-python-gpu-12.9/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-12.9/install-jupyter.bash b/saturnbase-python-gpu-12.9/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-12.9/install-jupyter.bash +++ b/saturnbase-python-gpu-12.9/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-gpu-12.9/install-miniconda.bash b/saturnbase-python-gpu-12.9/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-12.9/install-miniconda.bash +++ b/saturnbase-python-gpu-12.9/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-devel-11.8/environment.yml b/saturnbase-python-gpu-devel-11.8/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-devel-11.8/environment.yml +++ b/saturnbase-python-gpu-devel-11.8/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-devel-11.8/install-jupyter.bash b/saturnbase-python-gpu-devel-11.8/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-devel-11.8/install-jupyter.bash +++ b/saturnbase-python-gpu-devel-11.8/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-gpu-devel-11.8/install-miniconda.bash b/saturnbase-python-gpu-devel-11.8/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-devel-11.8/install-miniconda.bash +++ b/saturnbase-python-gpu-devel-11.8/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-devel-12.1/environment.yml b/saturnbase-python-gpu-devel-12.1/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-devel-12.1/environment.yml +++ b/saturnbase-python-gpu-devel-12.1/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-devel-12.1/install-jupyter.bash b/saturnbase-python-gpu-devel-12.1/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-devel-12.1/install-jupyter.bash +++ b/saturnbase-python-gpu-devel-12.1/install-jupyter.bash @@ -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 diff --git a/saturnbase-python-gpu-devel-12.1/install-miniconda.bash b/saturnbase-python-gpu-devel-12.1/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-devel-12.1/install-miniconda.bash +++ b/saturnbase-python-gpu-devel-12.1/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python-gpu-devel-12.9/environment.yml b/saturnbase-python-gpu-devel-12.9/environment.yml index 0302ba9..a3755a8 100644 --- a/saturnbase-python-gpu-devel-12.9/environment.yml +++ b/saturnbase-python-gpu-devel-12.9/environment.yml @@ -20,6 +20,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python-gpu-devel-12.9/install-jupyter.bash b/saturnbase-python-gpu-devel-12.9/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python-gpu-devel-12.9/install-jupyter.bash +++ b/saturnbase-python-gpu-devel-12.9/install-jupyter.bash @@ -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 ${CONDA_DIR}/ -type f,l -name '*.a' -delete diff --git a/saturnbase-python-gpu-devel-12.9/install-miniconda.bash b/saturnbase-python-gpu-devel-12.9/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python-gpu-devel-12.9/install-miniconda.bash +++ b/saturnbase-python-gpu-devel-12.9/install-miniconda.bash @@ -10,9 +10,9 @@ set -x && \ mkdir -p /opt && \ sh miniconda.sh -b -p /opt/saturncloud && \ rm miniconda.sh shasum && \ - /opt/saturncloud/bin/conda install -n base --override-channels -c conda-forge mamba==1.5.10 'python_abi=*=*cp*' --yes + /opt/saturncloud/bin/conda install -n base python=3.11.8 conda=24.9.2 libsqlite=3.51.1 sqlite=3.51.1 -c conda-forge && \ ln -s /opt/saturncloud/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ find /opt/saturncloud/ -follow -type f -name '*.a' -delete && \ find /opt/saturncloud/ -follow -type f -name '*.js.map' -delete && \ /opt/saturncloud/bin/conda clean -afy && \ - chown -R 1000:1000 /opt/saturncloud \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-python/Makefile b/saturnbase-python/Makefile index e5ab924..dfe7040 100644 --- a/saturnbase-python/Makefile +++ b/saturnbase-python/Makefile @@ -3,7 +3,6 @@ export build_image: docker build \ - --no-cache \ --build-arg JUPYTER_SATURN_VERSION=${JUPYTER_SATURN_VERSION} \ -t ${IMAGE} \ . diff --git a/saturnbase-python/environment.yml b/saturnbase-python/environment.yml index b315e38..75ce0ee 100644 --- a/saturnbase-python/environment.yml +++ b/saturnbase-python/environment.yml @@ -19,6 +19,8 @@ dependencies: - tornado - voila - yarl + - sqlite=3.51.1 + - libsqlite=3.51.1 - pip: - jupyter_server - jupyter_bokeh diff --git a/saturnbase-python/install-jupyter.bash b/saturnbase-python/install-jupyter.bash index 97646ce..914ecbe 100644 --- a/saturnbase-python/install-jupyter.bash +++ b/saturnbase-python/install-jupyter.bash @@ -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 diff --git a/saturnbase-python/install-miniconda.bash b/saturnbase-python/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-python/install-miniconda.bash +++ b/saturnbase-python/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-r-bioconductor/.env_deps b/saturnbase-r-bioconductor/.env_deps index 105af83..3aa21c2 100644 --- a/saturnbase-r-bioconductor/.env_deps +++ b/saturnbase-r-bioconductor/.env_deps @@ -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 diff --git a/saturnbase-r-bioconductor/Dockerfile b/saturnbase-r-bioconductor/Dockerfile index f023f76..8c03187 100644 --- a/saturnbase-r-bioconductor/Dockerfile +++ b/saturnbase-r-bioconductor/Dockerfile @@ -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 && \ diff --git a/saturnbase-r-bioconductor/install-miniconda.bash b/saturnbase-r-bioconductor/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-r-bioconductor/install-miniconda.bash +++ b/saturnbase-r-bioconductor/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-r-gpu/install-miniconda.bash b/saturnbase-r-gpu/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-r-gpu/install-miniconda.bash +++ b/saturnbase-r-gpu/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/saturnbase-r/Dockerfile b/saturnbase-r/Dockerfile index 6c3a0aa..4c77784 100644 --- a/saturnbase-r/Dockerfile +++ b/saturnbase-r/Dockerfile @@ -74,7 +74,7 @@ RUN apt-get -qq --allow-releaseinfo-change update \ > /dev/null \ # Install rstudio-server \ && apt-get install --yes --no-install-recommends libssl-dev > /dev/null \ - && curl -o rstudio.deb https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb \ + && curl -o rstudio.deb https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2025.09.2-418-amd64.deb \ && sudo gdebi --non-interactive rstudio.deb \ && rm rstudio.deb \ && sudo apt purge \ diff --git a/saturnbase-r/install-miniconda.bash b/saturnbase-r/install-miniconda.bash index a729ef9..ab3d912 100644 --- a/saturnbase-r/install-miniconda.bash +++ b/saturnbase-r/install-miniconda.bash @@ -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 \ No newline at end of file + chown -R 1000:1000 /opt/saturncloud diff --git a/scripts/sync.sh b/scripts/sync.sh index 74f9a6a..96c2d79 100644 --- a/scripts/sync.sh +++ b/scripts/sync.sh @@ -1,4 +1,5 @@ cp ./common/install-miniconda.bash ./saturnbase-python/install-miniconda.bash +cp ./common/install-miniconda.bash ./saturnbase-python-amd-gpu-devel/install-miniconda.bash cp ./common/install-miniconda.bash ./saturnbase-python-gpu-12.1/install-miniconda.bash cp ./common/install-miniconda.bash ./saturnbase-python-gpu-12.9/install-miniconda.bash cp ./common/install-miniconda.bash ./saturnbase-python-gpu-devel-12.1/install-miniconda.bash