diff --git a/Dockerfile b/Dockerfile index f7fe884a578485471a569d5a35f5549aeb76fe4f..2f3cb9d7a9f17d998496e5ac5d23511e2c208ed8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM renku/renkulab:renku0.9.1-py3.7-0.5.2 +FROM renku/renkulab:renku0.9.1-r3.6.1-0.5.2 # For some reason need to be root to install from symlink COPY src /code/src @@ -8,18 +8,35 @@ RUN ln -s /code/src # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # -# USER root -# RUN apt-get update && \ -# apt-get install -y --no-install-recommends \ -# apt-utils \ -# vim -# USER ${NB_USER} +USER root + +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + apt-utils \ + dirmngr \ + gpg-agent \ + less \ + libcurl4-openssl-dev \ + libxml2-dev \ + libz-dev \ + software-properties-common + +RUN chmod -R 777 /usr/local/lib/R/site-library + +USER ${NB_USER} # install the python dependencies USER root COPY requirements.txt environment.yml /tmp/ RUN conda env update -q -f /tmp/environment.yml && \ - /opt/conda/bin/pip install -r /tmp/requirements.txt && \ + /opt/conda/bin/pip install --ignore-installed -r /tmp/requirements.txt && \ conda clean -y --all && \ - conda env export -n "root" + conda env export -n "root" && \ + jupyter lab build USER ${NB_USER} + +# install the R dependencies +COPY install.R /tmp/ +RUN R -f /tmp/install.R + +RUN pipx upgrade renku diff --git a/covid-19-public-data.Rproj b/covid-19-public-data.Rproj new file mode 100644 index 0000000000000000000000000000000000000000..8e3c2ebc99e2e337f7d69948b93529a437590b27 --- /dev/null +++ b/covid-19-public-data.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/install.R b/install.R new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/requirements.txt b/requirements.txt index 47d15054f7b5c0ddc410938d746e610f522b0b8a..d05293f9bb3bbe4cccce6fece1282633e991d91a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -33,6 +33,7 @@ json5==0.9.0 jsonschema==3.2.0 jupyter-client==6.0.0 jupyter-core==4.6.3 +jupyter-rsession-proxy==1.1 jupyter-telemetry==0.0.5 jupyterhub==0.9.6 jupyterlab==1.2.5