Merge pull request hms-dbmi-cellenics#340 from hms-dbmi-cellenics/use…

…-virtualenv

switch to virtualenv

pipeline-runner/Dockerfile

@@ -37,14 +37,6 @@ RUN Rscript restore_renv.R
 # deactivate so that .libPaths used (set above)
 RUN R -q -e "renv::deactivate()"
 
-# install miniconda and geosketch
-# clean conda
-ENV RETICULATE_MINICONDA_PATH=/src/r-miniconda
-RUN R -q -e "reticulate::install_miniconda()" && \
-    R -q -e "reticulate::conda_install('r-reticulate', c('geosketch==1.2', 'scanorama==1.7.3'), pip = TRUE)" && \
-    CONDA_PATH=$(R -q -s -e "cat(reticulate::conda_binary())") && \
-    $CONDA_PATH clean --force-pkgs-dirs -y
-
 # use renv::snapshot() while R dependency updates are quick to build
 COPY ./renv.lock .
 RUN Rscript restore_renv.R
@@ -66,19 +58,22 @@ RUN Rscript check_package_licenses.R
 # ---------------------------------------------------
 FROM rocker/r-ver:4.2.2 AS common
 WORKDIR /src/pipeline-runner
-ENV RETICULATE_MINICONDA_PATH=/src/r-miniconda
 
 # get source code and R packages
 COPY --from=builder /src /src
 
 # add renv library to .libPaths
 ENV RENV_LIB=/src/lib
 RUN echo ".libPaths(c('$RENV_LIB', .libPaths()))" >> $(R RHOME)/etc/Rprofile.site && \
-    echo "python3-pip" >> sysdeps_run.txt && \
-    echo "wget" >> sysdeps_run.txt && \
+    echo "python3-pip python3-venv python3-dev wget" >> sysdeps_run.txt && \
     cat sysdeps_run.txt | xargs ./install_debian_packages.sh && \
     rm -rf *
 
+# install python packages in virtualenv
+ENV WORKON_HOME=/src/.virtualenvs
+RUN R -q -e "reticulate::virtualenv_create('r-reticulate')" && \
+    R -q -e "reticulate::virtualenv_install('r-reticulate', c('geosketch==1.2', 'scanorama==1.7.3'), pip_options='--no-cache-dir')" 
+
 # ---------------------------------------------------
 # PRODUCTION BUILD
 # ---------------------------------------------------