tranSMART-Foundation/transmart-gwas-plugin

Name: transmart-gwas-plugin

Owner: tranSMART Foundation

Description: The transmart (and grails) plugin that contains the GWAS elements.

Forked from: transmart/transmart-gwas-plugin

Created: 2015-09-09 14:07:44.0

Updated: 2016-02-03 14:16:25.0

Pushed: 2017-02-05 11:47:30.0

Homepage: null

Size: 143180

Language: PLSQL

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README

//GWAS Related Configuration: com.recomdata.dataUpload.appTitle=“Upload data to tranSMART (GPL)” com.recomdata.dataUpload.templates.dir=“/home/transmart/templates/” com.recomdata.dataUpload.uploads.dir=“/vol1/transmart/uploads/” com.recomdata.dataUpload.adminEmail=“mailto:DL-tranSMART_Support@transmartfoundation.org” com.recomdata.dataUpload.etl.dir=“/vol1/transmart/ETL/” com.recomdata.dataUpload.stageScript=“run_analysis_stage”

// Folder Manager com.recomdata.FmFolderService.importDirectory = '/vol1/transmart/import' com.recomdata.FmFolderService.filestoreDirectory = '/vol1/transmart/filestore' //Mail Configuration

grails.mail.host = “mailhub.transmartFoundation.org” grails.mail.port = 25 grails.mail.props = [“mail.smtp.auth”:“false”, “mail.smtp.starttls.enable”:“true”] // grails.mail.props = [“mail.smtp.auth”:“false”, // “mail.smtp.socketFactory.port”:“25”, // “mail.smtp.socketFactory.class”:“javax.net.ssl.SSLSocketFactory”, // “mail.smtp.socketFactory.fallback”:“false”] grails.mail.default.from = “DL-tranSMART_Support@transmartfoundation.org” grails.mail.attachments.dir = “/home/transmart/export”

//GWAS Related Configuration: com.recomdata.dataUpload.appTitle=“Upload data to tranSMART (GPL)” com.recomdata.dataUpload.templates.dir=“/home/transmart/templates/” com.recomdata.dataUpload.uploads.dir=“/vol1/transmart/uploads/” com.recomdata.dataUpload.adminEmail=“mailto:DL-tranSMART_Support@transmartfoundation.org” com.recomdata.dataUpload.etl.dir=“/vol1/transmart/ETL/” com.recomdata.dataUpload.stageScript=“run_analysis_stage”

// Folder Manager com.recomdata.FmFolderService.importDirectory = '/vol1/transmart/import' com.recomdata.FmFolderService.filestoreDirectory = '/vol1/transmart/filestore' //Mail Configuration

grails.mail.host = “mailhub.transmartFoundation.org” grails.mail.port = 25 grails.mail.props = [“mail.smtp.auth”:“false”, “mail.smtp.starttls.enable”:“true”] // grails.mail.props = [“mail.smtp.auth”:“false”, // “mail.smtp.socketFactory.port”:“25”, // “mail.smtp.socketFactory.class”:“javax.net.ssl.SSLSocketFactory”, // “mail.smtp.socketFactory.fallback”:“false”] grails.mail.default.from = “DL-tranSMART_Support@transmartfoundation.org” grails.mail.attachments.dir = “/home/transmart/export”

Update run_analysis_stage, load_analysis_stage.sh, move_analysis_to_biomart.sh, nightly_processing.sh to point to the respective directories of the scripts. ADD FMAPP configuration to kettle.properties:

FMAPP_DB_SERVER=dbserver.com FMAPP_DB_PORT=1524 FMAPP_DB_USER=fmapp FMAPP_DB_PWD=fmapp

Update ARCHIVE_DIR variable in Kettle-ETL/load_analysis_from_lz_to_staging.kjb

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.