Adding ubuntu docker build + instructions

docker/Dockerfile

@@ -0,0 +1,38 @@
+# Use 16.04 as it is the current linux default in the travis build 
+# https://github.com/fastlmm/FaST-LMM/blob/master/.travis.yml
+FROM ubuntu:16.04
+
+# gcc and g++ are critical dependencies for pysnptools
+RUN apt-get update && \
+  apt-get install -y wget gcc g++ && \
+  rm -rf /var/lib/apt/lists/*
+
+# Install conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.7.12-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh && \
+    /opt/conda/bin/conda clean -tipsy && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc && \
+    find /opt/conda/ -follow -type f -name '*.a' -delete && \
+    find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
+    /opt/conda/bin/conda clean -afy && \
+    chown -R $USERNAME:$USERNAME /opt/conda
+
+# Initialize environment
+ENV PATH /opt/conda/bin:$PATH
+RUN conda create -n fastlmm python=3.7
+RUN conda init bash
+RUN echo "conda activate fastlmm" >> ~/.bashrc
+ENV PATH /opt/conda/envs/fastlmm/bin:$PATH
+RUN conda install -n fastlmm "mkl==2019.4" "scipy>=1.1.0" "numpy>=1.11.3" jupyter
+
+# While not ideal, pysnptools/fastlmm should be installed separately via pip
+# See: https://github.com/fastlmm/FaST-LMM/issues/6#issuecomment-598458316
+RUN /opt/conda/envs/fastlmm/bin/pip install pysnptools --no-use-pep517
+RUN /opt/conda/envs/fastlmm/bin/pip install fastlmm
+
+# Initialize some working directory for bind mounts
+RUN mkdir /work
+WORKDIR /work

docker/README.md

@@ -0,0 +1,24 @@
+## Docker Instructions
+
+To build the docker container, run:
+
+```bash
+cd FaST-LMM/docker
+docker build -t fastlmm .
+```
+
+The container has no entry point but jupyter will be installed so
+a common use case for execution is:
+
+```bash
+# Mount local repo copy for access to datasets
+REPO_DIR=$HOME/repos/FaST-LMM
+docker run --rm -p 8888:8888 -it \
+-v $REPO_DIR:/work/FaST-LMM \
+fastlmm /bin/bash
+
+# In container:
+(fastlmm)> jupyter notebook --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''
+
+# Use notebook at localhost:8888
+```

tests/notebooks/synth-01/README.md

@@ -0,0 +1,5 @@
+### FaST-LMM Synthetic Data Export 01
+
+Export results and data from first example in: https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb
+
+The model parameterization is modified slightly in this case to disable LOCO fitting for proximal contamination control as well as heritability parameter optimization (the parameter is provided rather than optimized for).  This should make discrepancies with alternative implementations smaller.