Pipeline Builder for NGS tools Files

Readme File for Pipeline Builder R1V3

Pipeline Builder is a scripting tool for managing complex NGS analysis pipelines. It helps the user in composing NGS tool commands and composing his own analysis pipeline. It allows for data independent reproducible analysis creating protected environment which separates data from results through variable exportation. It comes as a command-line tool with a wizard menus and step-by-step tutorials.

An updated version of the original paper is still pending. I apologise for the inconvenience this might cause. In the mean time, you may refer to the following How-To.

[0] Installation

Having a pipeline_builder_{latest-version}.tar.gz file located in Desktop directory

    $ cd Desktop
    $ tar xfz pipeline_builder_{latest-version}.tar.gz
    $ cd pipeline_builder_{latest-version}

[1] Executing of the program

    $ ./pipeline_builder.pl

[2] Initialization .hconf file (Header file Initialization)

The header file contains all the information required to run the pipeline. It is strictly mandatory.

    $ ./pipeline_builder.pl --header

Fill in the request with appropriate data related to your pipeline

[3] Command list composition

The program guides the user to complete the list of command he needs to execute in the pipeline. Header file (.hconf) created at [2] is required.

    $ ./pipeline_builder.pl --build name-of-the-header-file-created.hconf

The user is guided in the composition. Follow the instruction showed. At the end of the composition type:

    CMD> s

For an unattended command composition type:

    CMD> m

[4] Global variables

In order to create global variables to be added to commands in recursive way call pipeline builder as follows:

i.e. Defining a personalized directory path

    $ ./pipeline_builder.pl --define name-of-the-header-file-created.hconf name-variable path-personalized-directory/

[5] Check variables

In order to generate a preview of the pipeline with all the composed commands ready to be executed (the global variables will be substituted with their values).

    $ ./pipeline_builder.pl --rebuild name-of-the-header-file-created.hconf

[6] Loading pipeline

In order to load the header file with commands and execute them.

    $ ./pipeline_builder.pl --load-pipeline name-of-the-header-file-created.hconf u

the option at the end of the command specifies which set of variables are required to complete the building

• u = user variables (specified at point [4])
• s = standard variables included in the program (default option)