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INSTALL.md

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Installation

  1. Clone

Assumes you already have git installed. If not you will need to get it installed by your system administrator.

git clone https://githubusername@github.com/VDBWRAIR/ngs_mapper.git
cd ngs_mapper
  1. Install System Packages

This is the only part of the installation process that you should need to become the super user

  • Red Hat/CentOS(Requires the root password)

    su -c 'python setup.py install_system_packages && chmod 666 setuptools*'

  • Ubuntu

    sudo 'python setup.py install_system_packages && chmod 666 setuptools*'
  1. Configure the defaults

You need to configure the ngs_mapper/config.yaml file.

  1. Copy the default config to config.yaml
```
cp ngs_mapper/config.yaml.default ngs_mapper/config.yaml
```
  1. Then edit the config file which is in yaml(http://docs.ansible.com/YAMLSyntax.html) format
The most important thing is that you edit the NGSDATA value so that it contains the path to your NGSDATA directory
  1. Python

The ngs_mapper requires python 2.7.3+ but < 3.0

python setup.py install_python

  • Quick verify that Python is installed

    The following should return python 2.7.x(where x is somewhere from 3 to 9)

    $HOME/bin/python --version

  1. Setup virtualenv

  2. Where do you want the pipeline to install? Don't forget this path, you will need it every time you want to activate the pipeline

```
venvpath=$HOME/.ngs_mapper
```
  1. Install the virtualenv to the path you specified
```
wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz#md5=f61cdd983d2c4e6aeabb70b1060d6f49 -O- | tar xzf -
$HOME/bin/python virtualenv-1.11.6/virtualenv.py --prompt="(ngs_mapper) " $venvpath 
```
  1. Activate the virtualenv. You need to do this any time you want to start using the pipeline
```
. $HOME/.ngs_mapper/bin/activate
```
  1. Install the pipeline into virtualenv
python setup.py install

It should be safe to run this more than once in case some dependencies do not fully install.

  1. Verify install

You can pseudo test the installation of the pipeline by running the functional tests

nosetests ngs_mapper/tests/test_functional.py

Back to the README.md