Installing and running

You can easily install SMRT Link and run it inside the container using the bash functions in management_tools.sh.

The SMRT Link installer

The install process consists of three steps:

1. Extraction
2. Configuration
3. Installation

These three steps can be carried out simply by executing the *.run file found in the ZIP file downloaded from PacBio's website. This approach requires the user to respond to several prompts to provide configuration details. However, this is not the approach taken here.

This repository contains a script install.sh which is executed from within the container which allows the user to install SL.

Configure install using variables

imported/install.sh script depends on the contents found within certain environment variables which are loaded into the container's environment. This gives you control over which options are passed to the SL installer.  

Modify behavior of bash functions using variables

Some bash functions are configured using environment variables.  

Install steps

1. Load the bash functions into your shell's environment using . management_tools.sh.
2. Build the image file using build. Skip if the image file is already built.
3. Run the container in the foreground, executing the install script within using install. Respond to the prompts.
4. If installation was successful, run the container in the background using start