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

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    "# Setup of Python Environment for GWAS-Lectures\n",
    "\n",
    "We will be using [limix](https://github.com/limix/limix) for the GWAS-lectures.   \n",
    "Limix is a flexible and efficient linear mixed-model library with interfaces to Python.  \n",
    "\n",
    "Assuming that Python is installed on the system the following sections describe how to install limix and all it's dependencies. \n",
    "\n",
    "## Install conda\n",
    "\n",
    "We will be using the open source package manager [conda](https://conda.io/docs/) to intall limix and jupyter notebook in a conda environment. Conda allows users to manage multiple environments with different package versions and can not only install python libraries but also various non-python software packages.  \n",
    "\n",
    "There are two ways to install conda:\n",
    " * [Anaconda](https://www.anaconda.com/) (kitchensink containing optimized scientific R and python libraries)\n",
    " * [Miniconda](https://conda.io/miniconda.html) (minimal installer for conda)\n",
    " \n",
    "We will use miniconda to install conda on our laptops. Navigate to https://conda.io/miniconda.html and download the version for your Operating System.\n",
    "\n",
    "### Install conda on MacOS\n",
    "\n",
    "```bash\n",
    "curl https://repo.anaconda.com/miniconda/Miniconda2-latest-MacOSX-x86_64.sh --output Miniconda2-latest-MacOSX-x86_64.sh\n",
    "bash Miniconda2-latest-MacOSX-x86_64.sh\n",
    "```\n",
    "\n",
    "### Install conda on Linux\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",
    "### Install conda on Windows (WSL)\n",
    "\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",
    "$ source activate gwas-lecture\n",
    "$ jupyter notebook\n",
    "```\n",
    "Open link that is displayed in terminal in browser \n",
    "\n",
    "***"
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    "## To run R in jupyter, install IRkernel\n",
    "\n",
    "The installation instructions for IRkernel are described in detail [here](https://github.com/IRkernel/IRkernel) or [here](https://irkernel.github.io/installation/#source-panel). Start by opening R in the terminal.\n",
    "\n",
    "In the terminal, type:\n",
    "* install.packages('IRkernel')\n",
    "* IRkernel::installspec()  # to register the kernel in the current R installation"
   ]
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