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Last pushed: a month ago
Short Description
Java based web front end to the pmart-omicsR back-end (http://pmart.labworks.org/)
Full Description

A Java based web front-end to the omicsR back-end to provide interactive visualization to the functions that service provides.

The web front-end uses the following 3rd-party tools

  • Spring Framework
  • Bootstrap CSS/JS UI framework
  • HighCharts for charting

Sample docker-compose.yml

To run the entire PMart application using docker-compose here is a sample docker-compose.yml to get it running in any docker compatible environment.

Tips for running PMart

  1. Google Analytics tracking can be disabled by removing the -Dpmart.google-analytics=true from the web environment property We encourage the usage of the google analytics as it helps us see usage of our work; but security is more important
  2. Adjust volumes accordingly to support logging on the Docker host
  3. Modify memory settings via -Xmx in the Java environment that are appropriate for the Docker host.

    docker-compose.yml

    omicsr:
    image: pnnl/pmart-omicsr-serve:latest
    command: "/usr/bin/Rscript start-rserve.R"
    ports:
     - "6311:6311"
    web:
    image: pnnl/pmart-web:latest
    links:
     - omicsr
    environment: 
     - "JAVA_OPTS=-Djava.awt.headless=true -Dpmart.google-analytics=true -Dpmart-r-serve=omicsr -Xms512M -Xmx2g -server -XX:+UseParallelGC"
    ports:
     - "80:8080"
    volumes: 
     - /var/log/tomcat:/usr/local/tomcat/logs
    

Licensing Information

P-Mart

Copyright © 2016, Battelle Memorial Institute All rights reserved.
  1. Battelle Memorial Institute (hereinafter Battelle) hereby grants permission to any person or entity lawfully obtaining a copy of this software and associated documentation files (hereinafter “the Software”) to redistribute and use the Software in source and binary forms, with or without modification. Such person or entity may use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and may permit others to do so, subject to the following conditions:
    • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.
    • 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.
    • Other than as used herein, neither the name Battelle Memorial Institute or Battelle may be used in any form whatsoever without the express written consent of Battelle.
    • Redistributions of the software in any form, and publications based on work performed using the software should include the following citation as a reference:
  2. 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 BATTELLE 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.
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pnnl

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