Install

Requirements

Hardware

  • CPU
    • Quad Core 2.5GHz or better
      • More cores = faster run time when running multiple samples
      • Faster GHz = faster each sample runs
  • RAM

    • This really depends on your data size

      If you are analyzing a 96 sample run then you should be fine with 1GB per CPU core

      If you are analyzing a 24 sample run then you will probably need about 4GB per CPU core since there will be more data

Python Packages

The pipeline comes with all of the necessary python packages already defined inside of requirements.txt as well as requirements-py26.txt

System Packages

The pipeline requires some system level packages(software installed via your Linux distribution’s package manager). The installer looks for system_packages.lst and installs the correct packages using that file. This file is a simple json formatted file that defines packages for some common Linux distrubutions(CentOS, Red Hat and Ubuntu).

Roche Utilities

If you intend on using the roche_sync you will need to ensure that the sfffile command is in your PATH. That is, if you execute $> sfffile it returns the help message for the command.

This command should automatically be installed and put in your path if you install the Data Analysis CD #3 that was given to you with your Roche instrument.

MidParse.conf

If you inted on using the roche_sync you may need to edit the included ngs_mapper/MidParse.conf file before installing. This file is formatted to be used by the Roche utilities and more information about how it is used can be found in the Roche documentation.

Installation

  1. Clone/Download the version you want

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

    1. Set your github username

      githubuser='mygithubusername'

    2. Clone the code

      git clone https://${githubuser}@github.com/VDBWRAIR/ngs_mapper.git
cd ngs_mapper

    3. Check which versions are available

      git tag

    4. Checkout the version you want(current version 1.2.2)

      git checkout -b vX.Y.Z vX.Y.Z

  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'

    • Ubuntu

      sudo python setup.py install_system_packages

  2. 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

    2. Then edit the ngs_mapper/config.yaml file which is in yaml format

      The most important thing is that you edit the NGSDATA value so that it contains the path to your NGSDATA directory.

      The path you use for NGSDATA must already exist

      mkdir -p /path/to/NGSDATA

  3. Python

    The ngs_mapper requires python 2.6 or 2.7

    • Quick verify that the correct version of Python is installed

      The following should return python 2.6.x or 2.7.x

      python --version

    • Install supported Python version into your home directory

      This is only needed if you do not have python 2.6.x or 2.7.x already. Red Hat/CentOS comes pre-shipped with Python 2.6.6 and the latest versions of Ubuntu come with 2.7.x so this is likely not needed.

      If the above command does not return 2.6.x or 2.7.x and you think it should, there is a chance that the system installed python is not first in your environment’s PATH.

      Here we specify to install into our home directory and to install Python version 2.7.10. You can specify anywhere you want and any version(less than 3.0), but you will need to then specify the path to that python later on.

      python setup.py install_python --prefix $HOME --version 2.7.10

  4. Setup virtualenv

    1. 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

    2. 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 -
python virtualenv-1.11.6/virtualenv.py --prompt="(ngs_mapper) " $venvpath

      If you had to install your own version of python above, you will need to use $HOME/bin/python instead of just python in the command above.

    3. Activate the virtualenv. You need to do this any time you want to start using the pipeline

      . ${venvpath}/bin/activate

  5. 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.

Build and view complete documentation

cd doc
make clean && make html
firefox build/html/install.html#build-and-view-complete-documentation
cd ..

Verify install

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

nosetests ngs_mapper/tests/test_functional.py