Using Omics Pipe

Omics Pipe is a Python framework for automating ‘best practice’ next generation sequencing pipelines. Omics Pipe can be run from the command-line by providing it with a YAML parameter file specifying your directory structure and software specific parameters. This executes a parallel automated pipeline on a Distributed Resource Management system (local cluster or Amazon Web Services (AWS)) that efficiently handles job resource allocation, monitoring and restarting. The goals of Omics Pipe are to provide researchers with an open-source computational solution to implement ‘best practice’ pipelines with minimal development overhead and providing visual outputs to aid the researcher in biological interpretation.

To install Omics Pipe, first determine if you are going to be using it on a local compute cluster or on AWS. If you are going to be installing it on your local cluster, follow the directions below (or have your system administrator install it globally). If you are going to create a local installation in your home directory on your cluster but you do not have administrative permissions, you can create a Python Virtual Environment and then follow the instructions below within the virtual environment.



  • Option 1: Install from pypi using pip:

    pip install omics_pipe
  • Option 2: Install from pypi using easy_install:

    easy_install omics_pipe
  • Option 3: Install from source: Download/extract the source code and run:

    python install
  • Option 4: Install the latest code directly from the repository:

    pip install -e hg+
  • Option 5: If you do not have administrator privileges on your system:

    Step 1: Set up a `Python Virtual Environment`_
    Step 2: Use one of the Options (1-4) above to install Omics Pipe within your virtual environment.


Once you have successfully installed Omics Pipe, you can run a pipeline by typing the command:

omics_pipe [-h] [--custom_script_path CUSTOM_SCRIPT_PATH]
          [--custom_script_name CUSTOM_SCRIPT_NAME]
                          [--compression {gzip, bzip}]
          {RNAseq_Tuxedo, RNAseq_count_based, RNAseq_cancer_report, RNAseq_TCGA, RNAseq_TCGA_counts, Tumorseq_MUTECT, miRNAseq_count_based, miRNAseq_tuxedo, WES_GATK, WGS_GATK, SomaticInDels, ChIPseq_MACS, ChIPseq_HOMER,  custom}

Running Omics Pipe on Amazon Web Services (AWS)

AWS Installation Instructions
Installation instructions for setting up the AWS Omics Pipe AMI


Step-by-step tutorial for running Omics Pipe
Creating a custom pipeline
Tutorial for creating and running a custom pipeline in Omics Pipe using existing modules
Adding new modules/tools
Tutorial for adding new modules to Omics Pipe be used in a custom pipeline

Version history

Version History


The latest copy of this documentation should always be available at:



Twitter: @kathleenfisch