diff --git a/flavors/vol2bird/environment.yaml b/flavors/vol2bird/environment.yaml index 4b5b6dc..36979b3 100644 --- a/flavors/vol2bird/environment.yaml +++ b/flavors/vol2bird/environment.yaml @@ -1,9 +1,70 @@ name: vol2bird channels: - conda-forge + - bioconda dependencies: - h5py - ipykernel - minio - webdavclient3 - git + - r-base + - hdf5 + - pkg-config + - gdal + - libgdal + - libgdal-hdf5 + - openssl + - proj + - gsl + - r-raster + - r-sf + - libexpat + - udunits2 + - bioconductor-rhdf5 + - r-labeling + - r-bit64 + - r-progress + - r-cli + - r-colorspace + - r-rcolorbrewer + - r-matrix + - r-fansi + - r-dotcall64 + - r-nlme + - r-munsell + - r-generics + - r-tibble + - r-spam + - r-maps + - r-isoband + - r-mgcv + - r-scales + - r-gtable + - r-utf8 + - r-munsell + - r-withr + - r-timechange + - r-clipr + - r-vroom + - r-tzdb + - r-stringi + - r-purrr + - r-curl + - r-dplyr + - r-fields + - r-ggplot2 + - r-jsonlite + - r-lubridate + - r-stringr + - r-tidyr + - r-tidyselect + - r-viridis + - r-readr + - r-gridextra + - r-classint + - r-s2 + - r-proxy + - r-sf + - r-wk + - r-udunits2 diff --git a/flavors/vol2bird/naavre-jupyter.Dockerfile b/flavors/vol2bird/naavre-jupyter.Dockerfile index de0e682..fd63c09 100644 --- a/flavors/vol2bird/naavre-jupyter.Dockerfile +++ b/flavors/vol2bird/naavre-jupyter.Dockerfile @@ -20,31 +20,20 @@ RUN rm /test_vol2bird.sh RUN rm version KNMI_vol_h5_to_ODIM_h5_out CMD vol2bird - -FROM ubuntu:22.04 AS biorad - -ARG DEBIAN_FRONTEND=noninteractive - -RUN apt update && apt upgrade && apt install -y libhdf5-dev libproj-dev gsl-bin libgsl-dev r-base-dev libudunits2-dev libgdal-dev gdal-bin r-bioc-rhdf5 -RUN R -e "install.packages('bioRad', repos='https://cran.r-project.org')" -RUN R -e "library('bioRad')" -RUN R -e "install.packages('generics', repos='https://cran.r-project.org')" - - FROM qcdis/n-a-a-vre:${NAAVRE_VERSION} ARG CONDA_ENV_FILE - COPY ${CONDA_ENV_FILE} environment.yaml RUN mamba env create -f environment.yaml +# RUN R -e "install.packages('suntools', repos='https://cran.r-project.org')" +# RUN R -e "install.packages('bioRad', repos='https://cran.r-project.org')" +# RUN R -e "library('bioRad')" + + COPY --from=vol2bird /opt/radar/ /opt/radar/ COPY --from=vol2bird /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/radar/lib:/opt/radar/rave/lib:/opt/radar/rsl/lib:/opt/radar/vol2bird/lib:/usr/lib/x86_64-linux-gnu ENV PATH=${PATH}:/opt/radar/vol2bird/bin:/opt/radar/rsl/bin -COPY --from=biorad /usr/local/lib/R/site-library /venv/lib/R/library - -RUN ldd --version -