Add Dockerfile and fix R notebook

Add installation description for docker

Author: timeu

Dockerfile

@@ -0,0 +1,19 @@
+FROM continuumio/miniconda
+
+RUN apt-get update --fix-missing  && apt-get install -y r-base && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+ADD environment.yml /tmp/environment.yml
+RUN conda env create -f /tmp/environment.yml
+
+RUN Rscript -e 'install.packages(c("IRkernel","lme4"),repos="https://cran.rstudio.com")'
+RUN /bin/bash -c "source activate gwas-lecture && Rscript -e 'IRkernel::installspec()'"
+
+# Pull the environment name out of the environment.yml
+RUN echo "source activate $(head -1 /tmp/environment.yml | cut -d' ' -f2)" > ~/.bashrc
+ENV PATH /opt/conda/envs/$(head -1 /tmp/environment.yml | cut -d' ' -f2)/bin:$PATH
+
+RUN mkdir /root/gwas-lecture
+COPY . /root/gwas-lecture
+
+EXPOSE 8888
+CMD ["/opt/conda/envs/gwas-lecture/bin/jupyter", "notebook", "--ip='0.0.0.0'","--allow-root","--port","8888","--no-browser","--notebook-dir","/root/gwas-lecture/"]

Lecture-0-Setup-of-Python-Environment.ipynb

@@ -46,11 +46,6 @@
     "```\n",
     "\n",
     "\n",
-    "#### Install conda on Windows \n",
-    "\n",
-    "Download EXE installer and install it.\n",
-    "\n",
-    "\n",
     "## Create a conda environment and install limix, jupyter notebook\n",
     "\n",
     "### For Linux, Mac OSX and WSL follow this:\n",
@@ -61,20 +56,17 @@
     "$ cd gwas-lecture\n",
     "$ conda env create -f environment.yml\n",
     "```\n",
-    "### For Windows follow this:\n",
     "\n",
-    "For Windows you also need the Windows Compiler for Python 2.7 which you can download [here](http://aka.ms/vcpython27) \n",
     "\n",
-    "```bash\n",
-    "$ git clone https://github.com/timeu/gwas-lecture.git \n",
-    "$ # or download archive from and extract it from https://github.com/timeu/gwas-lecture/archive/master.zip\n",
-    "$ cd gwas-lecture\n",
-    "$ conda create -n gwas-lecture python=3\n",
-    "$ activate gwas-lecture\n",
-    "$ conda install -c conda-forge cython numpy jupyter matplotlib hcephes\n",
-    "$ pip install liknorm numpy-sugar glimix-core joblib limix-legacy ncephes pandas-plink\n",
-    "$ pip install limix\n",
+    "## Docker container\n",
+    "\n",
+    "As a fallback if any of the installations above fail, it is possible to use a docker container that comes with all libraries pre-installed. First make sure to install [Docker](https://docs.docker.com/install/) on your machine.\n",
+    "Once docker is installed just run: \n",
+    "\n",
     "```\n",
+    "$ docker run -it timeu/gwas-lecture\n",
+    "```\n",
+    "Open http://localhost:8888 in your browser\n",
     "\n",
     "\n",
     "## Start jupyter notebook\n",
@@ -98,10 +90,7 @@
     "\n",
     "In the terminal, type:\n",
     "* install.packages('IRkernel')\n",
-    "* IRkernel::installspec()  # to register the kernel in the current R installation\n",
-    "\n",
-    "Launch jupyter with the specified kernel:\n",
-    "* jupyter console --kernel=ir"
+    "* IRkernel::installspec()  # to register the kernel in the current R installation"
    ]
   }
  ],

Lecture-6-BroadSenseHeritability.ipynb

@@ -69,9 +69,8 @@
    "source": [
     "## if lme4 isn't installed, install it first:\n",
     "if (!require(\"lme4\")) install.packages(\"lme4\");\n",
-    "\n",
     "library(lme4);\n",
-    "library(RLRsim);\n",
+    "\n",
     "source(\"data/cmeyer_glucs2015/hdr.estimate_r2_mixedmodels.R\");\n",
     "\n",
     "glucosinolateFileName <- \"data/cmeyer_glucs2015/bmeyer_etal.txt\";\n",