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Install zellkonverter env as rstudio user #974

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Install zellkonverter env as rstudio user #974

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11 changes: 8 additions & 3 deletions analyses/cell-type-wilms-tumor-06/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,13 @@ 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'); \
# Set basilisk directory and set for rstudio user
ENV BASILISK_EXTERNAL_DIR=/usr/share/basilisk
RUN mkdir -p ${BASILISK_EXTERNAL_DIR} && \
chown rstudio:rstudio ${BASILISK_EXTERNAL_DIR}
# install zellkonverter environment as rstudio user
RUN sudo -u rstudio \
Rscript -e "Sys.setenv(BASILISK_EXTERNAL_DIR = '${BASILISK_EXTERNAL_DIR}'); \
proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc); \
basilisk.utils::cleanConda()"
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