Update Dockerfile with viscose

deepspace/Dockerfile

@@ -1,30 +1,27 @@
-FROM rocker/geospatial:latest
-MAINTAINER "Miao Yu" [email protected]
+ARG CUDA_VERSION=12.6.0
+FROM nvidia/cuda:${CUDA_VERSION}-base-ubuntu24.04
 
-RUN apt-get update \
-  && R -e "BiocManager::install(c('duckdb','RNetCDF','Cardinal','CardinalWorkflows','RNiftyReg','ClusterR','purrr','imager','umap','Rtsne','Matrix','igraph','tidygraph','ggraph','reshape2','dbscan','MALDIquantForeign','fpc','future','patchwork','ggridges','pheatmap','distances','ropls'))" \
-  && installGithub.r \
-  yufree/rmwf \
-  yufree/enviGCMS \
-  yufree/pmd \
-  nhpatterson/RegCombIMS \
-  yufree/opentims/opentimsr \
-  yufree/HiTMaP \
-  && R -e "devtools::install_url('https://github.com/yufree/SimpleITKRInstaller/releases/download/v2.3.0/SimpleITK_2.3.0_R_x86_64-pc-linux-gnu.tar.gz',build=F)" \
-  && rm -rf /tmp/downloaded_packages \
-  && rm -rf /var/lib/apt/lists/* 
-
-WORKDIR /opt
-RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh -O anaconda3.sh && \
-    chmod +x anaconda3.sh
-
-RUN bash ./anaconda3.sh -b -p /opt/anaconda3 && \
-    rm ./anaconda3.sh && \
-    /opt/anaconda3/bin/conda create -yn timsconvert python=3.7
-
-ENV PATH /opt/anaconda3/bin/:$PATH
-SHELL ["conda", "run", "-n", "timsconvert", "/bin/bash", "-c"]
-RUN pip install --upgrade pip
-RUN git clone https://www.github.com/TheJacksonLaboratory/timsconvert
-RUN pip install -r timsconvert/requirements.txt
-RUN pip install h5py pandas numpy matplotlib
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y \
+    python3 \
+    python3-pip \
+    wget \
+    software-properties-common \
+    dirmngr
+
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-get update && apt-get install -y r-base r-base-dev
+RUN wget https://github.com/cdr/code-server/releases/download/v3.12.0/code-server_3.12.0_amd64.deb
+RUN dpkg -i code-server_3.12.0_amd64.deb
+RUN pip3 install jupyter ipykernel tables h5py numpy pandac scipy scikit-learn joblib matplotlib cupy-cuda12x
+RUN R -e "install.packages(c('IRkernel', 'tidyverse'), repos='http://cran.rstudio.com/')"
+RUN R -e "IRkernel::installspec(user = FALSE)"
+WORKDIR /workspace
+RUN code-server --install-extension ms-toolsai.jupyter
+RUN code-server --install-extension Ikuyadeu.r
+
+EXPOSE 8080
+
+CMD ["code-server", "--bind-addr", "0.0.0.0:8080"]