Mercury

About the Software

Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The local deployment at the BCM-HGSC handles analysis at terabyte scales, working reliably 24x7 all year round. Instructions to install Mercury on your local infrastructure is described below.

Also, we have ported Mercury onto the cloud, to allow researchers to test drive our pipeline without the need to install or configure anything. This is enabled using the DNAnexus platform.

Follow this link to start analyzing your samples right away! Login is required.

Quick Start Guide

For more detailed documentation, please read the included Word document Mercury_Pipeline_Documentation.doc

1. Install Valence (https://sourceforge.net/projects/valence/)

2. Unpack the provided tar ball. The location of the unpacked tar ball contents will now be refereed to as ${PIPELINE_HOME}

2a. Modify ${PIPELINE_HOME}/XML_protocols/ProductionPaths.csv to to fulfill program paths as appropriate

Some of the programs used in Mercury which must be defined in the above mentioned CSV can be found here: Interpreters that need to be installed include Perl, Ruby, and Python and the binaries to each are defined in the same CSV.

Another config file which needs to be modified is ${PIPELINE_HOME}/config/config_params.yml

More information about config_params.yml can be found in the Mercury_Pipeline_Documentation.doc document under section "2.3.3 Pipeline configuration parameters"

captureCode in config_params.yml can be found in ${PIPELINE_HOME}/tools/Capture_Metrics
bclToFastqPath needs to be downloaded from the Illumina website

3. To run the analysis pipeline starting from next-generation short-reads in FASTQ format, you can run the command:

ruby ${PIPELINE_HOME}/bin/DNASeq_BWA_Aligner.rb

It must be executed in the directory containing the FASTQ files. Refer to the section "2.3.2 Configuration file BWAConfigParams.txt" in the pipeline documents that describes the config file the above script will require.

4. To run the analysis pipeline starting from Illumina raw data (Bcl files) use script:

ruby ${PIPELINE_HOME}/bin/PreProcessor.rb

Download

Current release

Version 3.2

Download Mercury software and documentation

License

Copyright © Baylor College of Medicine Human Genome Sequencing Center. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE