diff --git a/Dockerfile b/Dockerfile index 20d60eb..e5394e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM jupyter/r-notebook:latest as builder -COPY /environment.yaml "${HOME}/" +COPY environment.yaml "${HOME}/environment.yaml" COPY --chown=1000:100 main "${HOME}/main" # Install python-related items @@ -18,15 +18,18 @@ RUN sed -i '/^python/d' /opt/conda/conda-meta/pinned && \ rm -rf "${HOME}/main/tests" # Remove tests, they are not required for running COMO # Update base environment -RUN mamba env update --name=base --file="${HOME}/environment.yaml" && \ - R -e "devtools::install_github('babessell1/zFPKM')" +RUN ls "${HOME}" && \ + mamba env update --name=base --file="${HOME}/environment.yaml" && \ + R -e "devtools::install_github('babessell1/zFPKM')" && \ + pip cache purge && \ + mamba clean --all --yes -FROM jupyter/r-notebook:latest +FROM jupyter/r-notebook:latestm COPY --from=builder ${HOME} ${HOME} RUN pip cache purge && \ - conda clean --all --yes --force-pkgs-dirs + conda clean --all --yes EXPOSE 8888 VOLUME /home/joyvan/main/data/local_files diff --git a/environment.yaml b/environment.yaml index 04588ff..707ac1a 100644 --- a/environment.yaml +++ b/environment.yaml @@ -35,7 +35,7 @@ dependencies: - conda-forge::python~=3.10 - conda-forge::r-base - conda-forge::r-biocmanager~=1.30.18 - - conda-forge::r-devtools~=2.4.3 + # - conda-forge::r-devtools~=2.4.3 - conda-forge::r-factominer~=2.8 - conda-forge::r-ggrepel~=0.9.1 - conda-forge::r-irdisplay~=1.1