Dockerfile used for various images being regularly used. These files …

…have been combined into a single repo for simpler maintainance.

au-eoed-dev-gamma/Dockerfile

@@ -0,0 +1,67 @@
+FROM ubuntu:latest
+
+LABEL authors="Pete Bunting"
+LABEL maintainer="[email protected]"
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH=/opt/miniconda/bin:$PATH
+
+RUN apt-get update --fix-missing && \
+    apt-get install -y apt-utils wget bzip2 ca-certificates curl git binutils vim libfftw3-dev gnuplot libgtk2.0-dev libgdal-dev libhdf5-dev libhdf5-100 libblas-dev libblas3 liblapack-dev liblapack3 liblapack-doc unzip make && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/miniconda && \
+    rm ~/miniconda.sh && \
+    /opt/miniconda/bin/conda clean -tipsy && \
+    ln -s /opt/miniconda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# Use python 3.7, update conda base and install AU-EOED software stack
+RUN conda install --yes -c conda-forge python=3.7; sync && conda update --yes -n base conda; sync && \
+    conda install --yes -c au-eoed -c conda-forge python=3.7 eodatadown arcsi rsgislib pb_process_tools sen1-ard-gamma compute-job-recorder scikit-learn scikit-image scikit-optimize scikit-plot scikit-fuzzy bayesian-optimization matplotlib pandas statsmodels h5py scipy rasterio shapely networkx sqlalchemy pycurl xgboost catboost lightgbm tpot seaborn ml_tooling cartopy numba pip sphinx elevation rtree luigi tqdm weasyprint jinja2; sync \
+    && chmod +x /opt/miniconda/bin/*; sync \
+    && conda clean --all -y; sync \
+    && conda clean -tipsy && sync
+
+RUN pip install pyod fiona geopandas schedule gsutil && sync
+
+# set gdal and proj data paths
+ENV GDAL_DATA=/opt/miniconda/share/gdal
+ENV PROJ_LIB=/opt/miniconda/share/proj
+
+RUN mkdir -p /opt/gamma
+WORKDIR /opt/gamma
+COPY GAMMA_SOFTWARE-20190613_MSP_ISP_DIFF_LAT.src.tar.gz /opt/gamma/GAMMA_SOFTWARE-20190613_MSP_ISP_DIFF_LAT.src.tar.gz
+RUN cd /opt/gamma && tar -zxf /opt/gamma/GAMMA_SOFTWARE-20190613_MSP_ISP_DIFF_LAT.src.tar.gz \
+    && rm /opt/gamma/GAMMA_SOFTWARE-20190613_MSP_ISP_DIFF_LAT.src.tar.gz 
+
+ENV GAMMA_HOME=/opt/gamma/GAMMA_SOFTWARE-20190613
+ENV MSP_HOME=$GAMMA_HOME/MSP \
+    ISP_HOME=$GAMMA_HOME/ISP \
+    DIFF_HOME=$GAMMA_HOME/DIFF \
+    DISP_HOME=$GAMMA_HOME/DISP \
+    LAT_HOME=$GAMMA_HOME/LAT
+
+ENV PATH=$PATH:$MSP_HOME/bin:$ISP_HOME/bin:$DIFF_HOME/bin:$LAT_HOME/bin:$DISP_HOME/bin:$MSP_HOME/scripts:$ISP_HOME/scripts:$DIFF_HOME/scripts:$LAT_HOME/scripts:$DISP_HOME/scripts \
+    HDF5_DISABLE_VERSION_CHECK=1 \
+    GNUTERM=qt \
+    GAMMA_RASTER="BMP" \
+    OS=linux64
+
+RUN cd $GAMMA_HOME/DISP/src; make -f makefile_static     \
+    && cd $GAMMA_HOME/DIFF/src; make -f makefile_static  \
+    && cd $GAMMA_HOME/ISP/src; make -f makefile_static   \
+    && cd $GAMMA_HOME/LAT/src; make -f makefile_static   \
+    && cd $GAMMA_HOME/ISP/src; make -f makefile_static   \
+    && sync
+
+# Add Tini
+ENV TINI_VERSION v0.18.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+ENTRYPOINT ["/tini", "--"]
+
+CMD [ "/bin/bash" ]

au-eoed-dev-spack/Dockerfile

@@ -0,0 +1,126 @@
+FROM     ubuntu:18.04
+
+LABEL    authors="Pete Bunting"
+LABEL    maintainer="[email protected]"
+
+ENV      LANG=C.UTF-8 LC_ALL=C.UTF-8 \
+         DEBIAN_FRONTEND=noninteractive \
+         HOME=/home/spack \
+         SPACK_ROOT=/home/spack/src/spack \
+         FORCE_UNSAFE_CONFIGURE=1
+
+
+RUN      apt-get -yqq update --fix-missing                 \
+      && apt-get -yqq install build-essential              \
+                              ca-certificates              \
+                              curl                         \
+                              g++                          \
+                              gcc                          \
+                              gfortran                     \
+                              git                          \
+                              gnupg2                       \
+                              make                         \
+                              python                       \
+                              unzip                        \
+                              apt-utils                    \
+                              autoconf                     \
+                              bzip2                        \
+                              vim                          \
+                              mercurial                    \
+                              sudo                         \
+                              gzip                         \
+                              tar                          \
+                              wget                         \
+                              binutils                     \
+                              coreutils                    \
+                              environment-modules          \
+      && apt-get clean                                     \ 
+      && rm -rf /var/lib/apt/lists/*                       \
+      && ln -s /usr/bin/tclsh8.6 /usr/bin/tclsh
+
+
+# Add non-privileged, but system docker user with sudo rights
+RUN        groupadd -r spack -g 901 && \
+           useradd -u 901 -r -m -g spack spack && \
+           echo "spack ALL=(root) NOPASSWD:ALL" > /etc/sudoers.d/spack && \
+           chmod 0440 /etc/sudoers.d/spack
+# this is also the user that executes all commands below
+USER       spack
+WORKDIR    $HOME
+
+COPY     packages.yaml .spack/packages.yaml
+RUN      sudo chown spack:spack -R $HOME
+
+# install spack
+RUN   mkdir -p $HOME/src/spack \
+      && git clone https://github.com/petebunting/spack.git $HOME/src/spack
+
+ENV      PATH=$SPACK_ROOT/bin:$PATH
+
+RUN spack install sqlite                        \
+    && spack install openblas                   \
+    && spack install python                     \
+    && spack install cmake                      \
+    && spack install py-numpy                   \
+    && spack install boost                      \
+    && spack install cgal                       \
+    && spack install py-scipy                   \
+    && spack install hdf5                       \
+    && spack install kealib                     \
+    && spack install gdal                       \
+    && spack install py-h5py                    \
+    && spack install py-chardet                 \
+    && spack install py-urllib3                 \
+    && spack install py-requests                \
+    && spack install py-nose                    \
+    && spack install py-matplotlib              \
+    && spack install py-pandas                  \
+    && spack install py-seaborn                 \
+    && spack install py-rasterio                \
+    && spack install py-networkx                \
+    && spack install py-scikit-image            \
+    && spack install py-scikit-learn            \
+    && spack install py-tpot                    \
+    && spack install py-ml-tooling              \
+    && spack install py-pyod                    \
+    && spack install py-xarray                  \
+    && spack install py-statsmodels             \
+    && spack install py-pycurl                  \
+    && spack install py-sqlalchemy              \
+    && spack install py-sphinx                  \
+    && spack install py-bokeh                   \
+    && spack install py-pyepsg                  \
+    && spack install py-openpyxl                \
+    && spack install py-psycopg2                \
+    && spack install py-fiona                   \
+    && spack install py-geopandas               \
+    && spack install py-flask                   \
+    && spack install py-numba                   \
+    && spack install py-rios                    \
+    && spack install py-python-fmask            \
+    && spack install sixs                       \
+    && spack install py-py6s                    \
+    && spack install py-google-cloud            \
+    && spack install py-planet                  \
+    && spack install py-opendatacube            \
+    && spack clean -a
+
+RUN spack install rsgislib                      \
+    && spack install py-arcsi                   \
+    && spack install py-compute-job-recorder    \
+    && spack install py-eodatadown              \
+    && spack clean -a
+
+
+# startup: force the use of a login shell
+COPY genentrypoint.sh $HOME/genentrypoint.sh
+RUN  /bin/bash $HOME/genentrypoint.sh 
+
+USER root
+RUN mv $HOME/entrypoint.sh /etc/entrypoint.sh \ 
+    && chmod a+x /etc/entrypoint.sh
+USER spack
+
+ENTRYPOINT ["/etc/entrypoint.sh"]
+CMD        ["/bin/bash"]
+

au-eoed-dev-spack/genentrypoint.sh

@@ -0,0 +1,136 @@
+#!/bin/bash -l
+
+. /usr/share/modules/init/sh
+. /home/spack/src/spack/share/spack/setup-env.sh
+
+spack load python
+spack load gdal
+spack load sixs
+spack load rsgislib
+spack load postgresql
+spack load hdf5
+spack load qhull
+spack load sqlite
+spack load py-affine
+spack load py-alabaster
+spack load py-arcsi
+spack load py-argparse
+spack load py-asn1crypto
+spack load py-attrs
+spack load py-babel
+spack load py-bokeh
+spack load py-bottleneck
+spack load py-cachetools
+spack load py-certifi
+spack load py-cftime
+spack load py-chardet
+spack load py-click
+spack load py-click-plugins
+spack load py-cligj
+spack load py-cloudpickle
+spack load py-compute-job-recorder
+spack load py-cycler
+spack load py-cython
+spack load py-dask
+spack load py-deap
+spack load py-decorator
+spack load py-docutils
+spack load py-eodatadown
+spack load py-et-xmlfile
+spack load py-fiona
+spack load py-flask
+spack load py-geopandas
+spack load py-gitdb
+spack load py-gitpython
+spack load py-google-auth
+spack load py-google-cloud
+spack load py-google-resumable-media-python
+spack load py-h5py
+spack load py-idna
+spack load py-imagesize
+spack load py-itsdangerous
+spack load py-jdcal
+spack load py-jinja2
+spack load py-joblib
+spack load py-jsonschema
+spack load py-kiwisolver
+spack load py-llvmlite
+spack load py-locket
+spack load py-markupsafe
+spack load py-matplotlib
+spack load py-ml-tooling
+spack load py-munch
+spack load py-netcdf4
+spack load py-networkx
+spack load py-nose
+spack load py-numba
+spack load py-numexpr
+spack load py-numpy
+spack load py-opendatacube
+spack load py-openpyxl
+spack load py-packaging
+spack load py-pandas
+spack load py-partd
+spack load py-patsy
+spack load py-pillow
+spack load py-pkgconfig
+spack load py-planet
+spack load py-protobuf
+spack load py-psycopg2
+spack load py-py6s
+spack load py-pyasn1
+spack load py-pycurl
+spack load py-pyepsg
+spack load py-pygments
+spack load py-pyod
+spack load py-pyparsing
+spack load py-pypeg2
+spack load py-pyproj
+spack load py-pysolar
+spack load py-python-dateutil
+spack load py-python-fmask
+spack load py-pytz
+spack load py-pywavelets
+spack load py-pyyaml
+spack load py-rasterio
+spack load py-requests
+spack load py-rios
+spack load py-rsa
+spack load py-scikit-image
+spack load py-scikit-learn
+spack load py-scipy
+spack load py-seaborn
+spack load py-setuptools
+spack load py-setuptools-scm
+spack load py-shapely
+spack load py-six
+spack load py-smmap
+spack load py-snowballstemmer
+spack load py-snuggs
+spack load py-sphinx
+spack load py-sphinx-rtd-theme
+spack load py-sphinxcontrib-websupport
+spack load py-sqlalchemy
+spack load py-statsmodels
+spack load py-stopit
+spack load py-toolz
+spack load py-tornado
+spack load py-tpot
+spack load py-tqdm
+spack load py-urllib3
+spack load py-vcversioner
+spack load py-werkzeug
+spack load py-xarray
+spack load python
+
+echo "#!/bin/bash -l" > /home/spack/entrypoint.sh
+echo ". /home/spack/src/spack/share/spack/setup-env.sh" >> /home/spack/entrypoint.sh
+echo "export PATH=$PATH" >> /home/spack/entrypoint.sh
+echo "export PYTHONPATH=$PYTHONPATH" >> /home/spack/entrypoint.sh
+echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> /home/spack/entrypoint.sh
+echo "export MANPATH=$MANPATH" >> /home/spack/entrypoint.sh
+echo "export LIBRARY_PATH=$LIBRARY_PATH" >> /home/spack/entrypoint.sh
+echo "export CPATH=$CPATH" >> /home/spack/entrypoint.sh
+echo "export PKG_CONFIG_PATH=$PKG_CONFIG_PATH" >> /home/spack/entrypoint.sh
+echo "export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH" >> /home/spack/entrypoint.sh
+echo 'exec "$@"' >> /home/spack/entrypoint.sh

au-eoed-dev-spack/packages.yaml

@@ -0,0 +1,21 @@
+packages:
+  python:
+    version: [3.7.4]
+    variants: +shared+tkinter+uuid
+  py-numpy:
+    variants: ^openblas
+  hdf5:
+    variants: +cxx+hl+shared~mpi
+  netcdf:
+    variants: ~mpi
+  py-h5py:
+    variants: ~mpi
+  gdal:
+    version: [3.0.1]
+    variants: +python+qhull+sqlite3+armadillo+geos+kea+hdf5+openjpeg+pg+netcdf
+  libsigcpp:
+    version: [2.9.3]
+
+
+
+

au-eoed-dev/Dockerfile

@@ -0,0 +1,43 @@
+FROM ubuntu:latest
+
+LABEL authors="Pete Bunting"
+LABEL maintainer="[email protected]"
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH=/opt/miniconda/bin:$PATH
+
+RUN apt-get update --fix-missing && \
+    apt-get install -y apt-utils wget bzip2 ca-certificates curl git binutils vim make && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/miniconda && \
+    rm ~/miniconda.sh && \
+    /opt/miniconda/bin/conda clean -tipsy && \
+    ln -s /opt/miniconda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# Use python 3.7, update conda base and install AU-EOED software stack
+RUN conda install --yes -c conda-forge python=3.7; sync && conda update --yes -n base conda; sync && \
+    conda install --yes -c au-eoed -c conda-forge python=3.7 eodatadown arcsi rsgislib pb_process_tools sen1-ard-gamma compute-job-recorder scikit-learn scikit-image scikit-optimize scikit-plot scikit-fuzzy bayesian-optimization matplotlib pandas statsmodels h5py scipy rasterio shapely networkx sqlalchemy pycurl xgboost catboost lightgbm tpot seaborn ml_tooling cartopy numba pip sphinx elevation rtree luigi tqdm weasyprint jinja2 keras keras-preprocessing pytables parallel plotly bokeh pygal jupyterlab psutil; sync \
+    && chmod +x /opt/miniconda/bin/*; sync \
+    && conda clean --all -y; sync \
+    && conda clean -tipsy && sync
+
+RUN pip install pyod fiona geopandas schedule gsutil cvxopt dropbox  && sync
+
+# set gdal and proj data paths
+ENV GDAL_DATA=/opt/miniconda/share/gdal
+ENV PROJ_LIB=/opt/miniconda/share/proj
+
+# Add Tini
+ENV TINI_VERSION v0.18.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+ENTRYPOINT ["/tini", "--"]
+
+CMD [ "/bin/bash" ]
+
+