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Install zellkonverter at system level #974

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472e2ab
Install zellkonverter env as rstudio user
jashapiro Jan 3, 2025
d9a8a94
Merge branch 'main' into jashapiro/basilisk-fix
jashapiro Jul 31, 2025
6028143
Use Basilisk system installs
jashapiro Jul 31, 2025
4553a9f
Change all zellkonverter installations
jashapiro Jul 31, 2025
6079e73
Merge branch 'main' into jashapiro/basilisk-fix
jashapiro Jul 31, 2025
5478734
Rearrange doublet dockerfile
jashapiro Jul 31, 2025
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9 changes: 3 additions & 6 deletions analyses/cell-type-neuroblastoma-04/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,11 @@ LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPC
# Set an environment variable to allow checking if we are in an OpenScPCA container
ENV OPENSCPCA_DOCKER=TRUE


# Disable the renv cache to install packages directly into the R library
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
# Install Basilisk python packages in the system library
ARG BASILISK_USE_SYSTEM_DIR=1

# set a name for the conda environment
ARG ENV_NAME=openscpca-cell-type-neuroblastoma-04
Expand Down Expand Up @@ -78,11 +81,5 @@ RUN Rscript -e 'renv::restore()' && \
rm -rf /tmp/downloaded_packages && \
rm -rf /tmp/Rtmp*

# Complete installation of zellkonverter conda env
ENV BASILISK_EXTERNAL_DIR=/usr/local/renv/basilisk
RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc); \
basilisk.utils::cleanConda()"

# Set CMD to bash to activate the environment for any commands
CMD ["/bin/bash"]
8 changes: 2 additions & 6 deletions analyses/cell-type-wilms-tumor-06/Dockerfile
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Expand Up @@ -14,6 +14,8 @@ ENV OPENSCPCA_DOCKER=TRUE

# Disable the renv cache to install packages directly into the R library
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
# Install Basilisk python packages in the system library
ARG BASILISK_USE_SYSTEM_DIR=1

# Install renv
RUN Rscript -e 'install.packages("renv")'
Expand All @@ -29,9 +31,3 @@ RUN Rscript -e 'renv::restore()' && \
rm -rf ~/.cache/R/renv && \
rm -rf /tmp/downloaded_packages && \
rm -rf /tmp/Rtmp*

# Complete installation of zellkonverter conda env
ENV BASILISK_EXTERNAL_DIR=/usr/local/renv/basilisk
RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc); \
basilisk.utils::cleanConda()"
28 changes: 12 additions & 16 deletions analyses/doublet-detection/Dockerfile
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Expand Up @@ -11,9 +11,21 @@ ARG ENV_NAME=openscpca-doublet-detection
# Set an environment variable to allow checking if we are in an OpenScPCA container
ENV OPENSCPCA_DOCKER=TRUE

# Disable the renv cache to install packages directly into the R library
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
# Install Basilisk python packages in the system library
ARG BASILISK_USE_SYSTEM_DIR=1

# set environment variables to install conda
ENV PATH="/opt/conda/bin:${PATH}"

# Install pandoc dependency
RUN apt-get -y update && \
DEBIAN_FRONTEND=noninteractive \
apt-get install --no-install-recommends -y \
pandoc \
&& rm -rf /var/lib/apt/lists/*

# Install conda via miniforge
# adapted from https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -o /tmp/miniforge.sh \
Expand All @@ -33,19 +45,9 @@ RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
RUN conda install --channel=conda-forge --name=base conda-lock \
&& conda clean --all --yes

# Install pandoc dependency
RUN apt-get -y update && \
DEBIAN_FRONTEND=noninteractive \
apt-get install --no-install-recommends -y \
pandoc \
&& rm -rf /var/lib/apt/lists/*

# Install renv
RUN Rscript -e "install.packages('renv')"

# Disable the renv cache to install packages directly into the R library
ENV RENV_CONFIG_CACHE_ENABLED=FALSE

# Copy conda lock file to image
COPY conda-lock.yml conda-lock.yml

Expand All @@ -68,11 +70,5 @@ RUN Rscript -e 'renv::restore()' \
&& rm -rf /tmp/downloaded_packages \
&& rm -rf /tmp/Rtmp*

# Complete installation of zellkonverter conda env
ENV BASILISK_EXTERNAL_DIR=/usr/local/renv/basilisk
RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc); \
basilisk.utils::cleanConda()"

# Set CMD to bash to activate the environment when launching
CMD ["/bin/bash"]
10 changes: 4 additions & 6 deletions analyses/simulate-sce/Dockerfile
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Expand Up @@ -43,7 +43,11 @@ RUN conda-lock install -n ${ENV_NAME} conda-lock.yml \
# Activate conda environment on bash launch
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc

# Disable the renv cache to install packages directly into the R library
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
# Install Basilisk python packages in the system library
ARG BASILISK_USE_SYSTEM_DIR=1

RUN Rscript -e "install.packages(c('remotes', 'renv'))"

WORKDIR /usr/local/renv
Expand All @@ -54,12 +58,6 @@ RUN Rscript -e "renv::restore()" && \
rm -rf /tmp/downloaded_packages && \
rm -rf /tmp/Rtmp*

# Complete installation of zellkonverter conda env
ENV BASILISK_EXTERNAL_DIR=/usr/local/renv/basilisk
RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc)"



# set final workdir for commands
WORKDIR /home