FROM registry.ethz.ch/eduit/images/notebooks/25fs/jh-notebook-base:5.2.1-01 USER root ####### # Julia ####### RUN http_proxy=http://proxy.ethz.ch:3128 https_proxy=http://proxy.ethz.ch:3128 julia -e "using Pkg; Pkg.add.([ \ \"NBInclude\", \ \"PyPlot\", \ \"Roots\", \ \"UnPack\", \ \"WhereTheWaterFlows\", \ \"BenchmarkTools\", \ \"Plots\" \ ]); Pkg.update;" #### # R #### RUN Rscript >/dev/null 2>&1 -e "install.packages(pkgs=c( \ 'bayesplot', \ 'bayestestR', \ 'blockmodeling', \ 'biostat3', \ 'brms', \ 'countrycode', \ 'GGally', \ 'ggforce', \ 'ggplot2', \ 'ggraph', \ 'goldfish', \ 'gt', \ 'gtsummary', \ 'igraph', \ 'lfe', \ 'lubridate', \ 'loo', \ 'matlib', \ 'mice', \ 'nloptr', \ 'openxlsx', \ 'RBGL', \ 'RColorBrewer', \ 'RcppEigen', \ 'RSiena', \ 'sbm', \ 'scico', \ 'sensitivity', \ 'sjPlot', \ 'sna', \ 'stargazer', \ 'statnet', \ 'terra', \ 'tibble', \ 'tidybayes', \ 'tidygraph', \ 'tidyverse'), repos=c('http://cran.r-project.org'), dependencies=TRUE, timeout=300)" \ && \ Rscript -e "install.packages(pkgs=c('BiocManager'), repos=c('http://cran.r-project.org'))" \ && \ Rscript -e "BiocManager::install()" \ && \ Rscript -e "devtools::install_github(repo = 'AECP-ETHZ/ETH.OLP')" ############################## # Python and R from Condaforge ############################## RUN conda config --set default_threads 4 && \ mamba install -q -c defaults -c conda-forge -c bioconda -c bokeh \ arviz \ autogluon \ biopython \ bokeh \ boost-histogram \ corner \ cobra \ dynesty \ emcee \ ete3 \ flax \ fqdn \ gdal==3.9.2\ graph-tool \ igraph \ ipydatagrid \ isoduration \ keras \ meshio \ mplcursors \ multi_rake \ optax \ pathos \ pint \ plotly \ pubchempy \ py3dmol \ pylatex \ pymatgen \ pymrio \ pyteomics \ pytesseract \ pyspellchecker \ rdkit \ root \ sinfo \ scanpy \ scikit-image \ scikit-learn \ seaborn \ sparqlwrapper \ sqlite==3.48.0 \ tabulate \ tinygp \ trame \ trame-vuetify \ uncertainties \ uri-template \ webcolors \ wikipedia \ wordcloud \ xgboost \ yake \ r-ape \ r-bio3d \ r-devtools \ r-gifski \ r-lpsolve \ r-lhs \ r-rsolnp \ && \ mamba install -c python-control control \ && \ mamba clean --all # pyvista \ # breaks sqlite3, hub fails to start ################## # Python from pypi ################## # Packages breaking Jupyter or other packages # brightway25 \ # ecoinvent-interface \ # mariopy \ # pypardiso \ RUN PIP_PROXY=http://proxy.ethz.ch:3128 pip3 install --proxy=http://proxy.ethz.ch:3128 --default-timeout=100 \ adjustText \ anndata \ asserts \ astroquery \ brainpy \ Cartopy \ deep_translator \ einsteinpy \ eppy \ geopandas \ gmsh \ goatools \ gseapy \ gurobipy \ jaxopt \ keybert \ langchain-openai \ lmfit \ mycolorpy \ mpl-interactions["jupyter"] \ mpl_point_clicker \ networkit \ networkx \ numdifftools \ obspy \ openai \ opencv-python opencv-contrib-python \ otter-grader \ petitRADTRANS \ pyvista \ zfit \ PyAstronomy \ pycosmo \ pycryptodome \ pyFAI \ rasterio \ rise \ sensemapi \ summa \ tensorflow \ "tensorflow-probability[jax]" \ # torch \ umap \ umap-learn \ vpython \ wiktionaryparser \ xgboost \ yolov5 # ===================== # Packages requested after semester start, should go to the list 2 RUNs above if a major rebuild is planned. # Placing it here keeps the image cache disk space low, because it adds only a thin extra layer # ===================== # No extra package added yet for FS25... # RUN PIP_PROXY=http://proxy.ethz.ch:3128 pip3 install -U --proxy=http://proxy.ethz.ch:3128 --default-timeout=100 \ # package_1 \ # package_last # User submitted support programs COPY bin /usr/local/bin/ # Configuration items COPY etc /etc USER 1000