Chapter 6 Instructions - Using the Command Line

This section describes how to use the command line to run the pipeline. This method will run the analysis from start to finsh by a single command, executed via the terminal.

6.1 Download the Repository

  1. Download the github repo and save the folder on your device. Find the CoMarker Github page here. The main folder must include the ‘Bash’, ‘Functions’ and ‘HTML Reports’ folders.

6.2 Input Parameters

  1. Edit param_fiji.txt and param_R.txt with the desired parameters and save.

6.3 Open a Terminal Window

  1. Open a terminal window.
  2. Change directory (cd) to the ‘CoMarker/Bash’ directory.
  3. Write sh full_run.sh.
  4. The output files will be saved in the folders specified in the parameters.

Note: The full_run.sh file works for mac OS; it can be adapted to windows by changing the path to the Fiji app.