sam-tools

Python pre-requisites:

1. Install Python header files. The package providing these files varies per distribution. For example:

• Fedora 20 provides header files in the python-devel package:

  yum install python-devel
  

2. Install pip:

   wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py
   python get-pip.py
   
   (or)
   
   sudo yum install python-pip
   

To run automated tests:

1. Get the source code and install dependencies:

   git clone git@github.com:sthirugn/sam-tools.git
   cd sam-tools
   pip install -r requirements.txt
   

2. Copy samtools.properties.sample and name it samtools.properties (referred to as the 'config file' in this doc). Update required parameters in the config file.

3. To see all the available tasks:

   fab --list
   

4. To run a specific task:

   fab -H <hostname> -u <user> create_org
   

5. You can specify the 'host' and 'user' options in the config file if you want to work with just one host as a single user. This done, the command becomes much simpler:

   fab create_org
   

Note: the 'user' config file option defaults to your current user.

Note: It is better to place your ssh public key in the host or add -p <password> to your fab command.

Code Contribution

1. git clone this repo

2. Make necessary code changes

3. Run local tests and validate the code

4. Make sure pylint and flake8 pass:

   make lint
   make flake8
   

Known Issues

If you are using rhel, you may find problems invoking fab command. Please check stackoverflow recommended solution (look for the solution which tells to comment out number.py) to fix this.