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

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

    1. Clone the code

      git clone https://github.com/VDBWRAIR/ngs_mapper.git
      cd ngs_mapper
      
    2. Check which versions are available

      git tag
      
    3. Checkout the version you want(current version 1.5.0)

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

    The project now comes with a much more simplified installer which is based on miniconda.

    The following will install the project into the current directory that you are in.

    ./install.sh miniconda
    
  4. PATH Setup

    Once the project is installed you will need to setup your PATH environmental variable to include the

    export PATH=$PWD/miniconda/bin:$PATH
    

    You can put this into your .bashrc file inside your home directory so that any time you open a new terminal it automatically is run.

    If you don’t setup your .bashrc you will have to run the export command from above every time you open a new terminal.

Verify install

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

ngs_mapper/tests/slow_tests.sh