Merge branch 'master' of https://github.com/timeu/gwas-lecture

in process of loading import-data notebook

Author: mahort

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

@@ -31,24 +31,44 @@
     "### Install conda on Linux\n",
     "\n",
     "```bash\n",
-    "curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh --output-file Miniconda2-latest-Linux-x86_64.sh\n",
-    "bash Miniconda2-latest-Linux-x86_64.sh\n",
+    "curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O Miniconda2-latest-Linux-x86_64.sh\n",
+    "sh Miniconda2-latest-Linux-x86_64.sh\n",
     "```\n",
     "\n",
-    "### Install conda on Windows\n",
+    "### Install conda on Windows (WSL)\n",
     "\n",
-    "Download EXE installer and install it.\n",
+    "The easiest way is to first install the [Windwos Subsystem for Linux (WSL)](https://docs.microsoft.com/en-us/windows/wsl/install-win10)\n",
+    "Once this is done start the Linux distrubition that was previously installed from the Start Menu\n",
+    "\n",
+    "```bash\n",
+    "curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O Miniconda2-latest-Linux-x86_64.sh\n",
+    "sh Miniconda2-latest-Linux-x86_64.sh\n",
+    "```\n",
     "\n",
     "\n",
     "## Create a conda environment and install limix, jupyter notebook\n",
     "\n",
+    "### For Linux, Mac OSX and WSL follow this:\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 env create -f environment.yml\n",
     "```\n",
     "\n",
+    "\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 -p 8888:8888 timeu/gwas-lecture\n",
+    "```\n",
+    "Open http://localhost:8888 in your browser and copy and paste the token for the docker run above\n",
+    "\n",
+    "\n",
     "## Start jupyter notebook\n",
     "\n",
     "```\n",
@@ -70,10 +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

@@ -13,6 +13,7 @@ To open these notebooks in Jupyter, download the files to a directory on your co
 Online read-only versions
 =========================
 
+
 Use the following links:
 
 * [Lecture-0 Setup of Python Environment](http://nbviewer.ipython.org/urls/raw.github.com/timeu/gwas-lecture/master/Lecture-0-Setup-of-Python-Environment.ipynb)

README.md

@@ -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/"]

data/BYxRM/BYxRM.hdf5

@@ -0,0 +1 @@
+install.packages("lme4")

data/arab107/atwell_107.hdf5

@@ -0,0 +1,2 @@
+r-2018-02-05
+python-2.7