thehyve/GWAVA

Name: GWAVA

Owner: The Hyve

Description: Genome Wide Association Study Visualizer (LODZ2 project)

Created: 2017-05-03 09:24:29.0

Updated: 2017-05-19 06:58:01.0

Pushed: 2017-07-26 08:46:06.0

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Size: 28460

Language: HTML

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README

Genome-Wide Association Visual Analyzer for tranSMART

This is an instruction of how to generate a gwava war file to work with 17.1 version of tranSMART. It relates to https://github.com/thehyve/transmart-core/ repository.

• Required libraries
• Configuration
• Generating a war file
• Test data

1. Required libraries

The following libraries must be present in /lib folder:

• commons-beanutils-1.8.3.jar
• commons-beanutils-bean-collections-1.8.3.jar
• commons-beanutils-core-1.8.3.jar
• commons-codec-1.6.jar
• commons-digester3-3.2.jar
• commons-digester3-3.2-javadoc.jar
• commons-lang3-3.1.jar
• commons-logging-1.1.1.jar
• httpclient-4.0.jar
• httpcore-4.2.1.jar
• itextpdf-5.3.4.jar
• jdom-2.0.6.jar
• jersey-client-1.4.jar
• jersey-core-1.4.jar
• jgoodies-common-1.3.1.jar
• jgoodies-looks-2.5.1.jar
• log4j-1.2.17.jar
• log4j-api-2.5.jar
• log4j-core-2.5.jar

2. Configuration

Settings required for tranSMART configuration file:

def gwavaEnabled??????= true
...
/* {{{ Spring Security configuration */    
grails { plugin { springsecurity {
    ...
    if (useRequestMap) { ... }
    else {
        def gwavaMappings = [
             [pattern: '/gwasWeb/**', access: ['IS_AUTHENTICATED_ANONYMOUSLY']],
        ]
        ...
        interceptUrlMap = [ ... ] +
        (gwavaEnabled ?  gwavaMappings : []) +
        [
            [pattern: '/**', access: ['IS_AUTHENTICATED_REMEMBERED']], // must be last
        ]
        ...
     }
     ...
}}}                
...
/* {{{ gwava */
if (org.transmartproject.app.gwavaEnabled) {
    // assume deployment alongside transmart
    com { recomdata { rwg { 
        webstart {
            def url       = new URL(org.transmartproject.app.transmartURL)
            codebase      = "$url.protocol://$url.host${url.port != -1 ? ":$url.port" : ''}/gwava"
            jar           = './ManhattanViz2.1k.jar'
            mainClass     = 'com.pfizer.mrbt.genomics.Driver'
            gwavaInstance = 'transmartstage'
            transmart.url = org.transmartproject.app.transmartURL - ~'\\/$'
       } 
       qqplots {
           cacheImages = jobsDirectory + '/cachedQQplotImages/'
           temporaryImageFolder = '/images/tempImages/'
           temporaryImageFolderFullPath = explodedWarDir + temporaryImageFolder
       }
       manhattanplots {
           cacheImages = jobsDirectory + '/cachedManhattanplotImages/'
           temporaryImageFolder = '/images/tempImages/'
           temporaryImageFolderFullPath = explodedWarDir + temporaryImageFolder
       }
   } } }
}
...

Settings for build.xml:

• Line 44: webstart.root property - should contain the URL of where the Gwava part will be deployed. It is already configured for the test instances and so is the war file.
• Line 87: keystore. properties - keystore details go at line.

3. Generating a war file

IMPORTANT! Oracle Java 7 Web Start (default webStartProvider for Linux) is working only when war is built using JAVA7

Run:

ant transmartwar 

War file will be created inside /dist folder.

4. Test data

17.1 tranSMART test data contains a study called MAGIC, however, it is not a part of basic transmart-data loading scripts. It can be loaded using transmart-batch. Check https://github.com/thehyve/transmart-core/tree/master/transmart-batch/ for more detailed instructions.

• to load MAGIC study with transmart-batch:

  ./transmart-batch.sh -p studies/MAGIC/gwas.params

• to load data for de_rc_snp_info table with transmart-batch:

  gradle functionalTestPrepare

License

Copyright © 2014-2017 Pfizer Inc.

Genome-Wide Association Visual Analyzer for tranSMART is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.