Name: transmart-gwas-plugin
Owner: TranSMART Project
Description: The transmart (and grails) plugin that contains the GWAS elements.
Created: 2014-02-12 21:14:28.0
Updated: 2016-05-26 13:47:03.0
Pushed: 2017-03-31 07:20:35.0
Homepage: null
Size: 143192
Language: PLSQL
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| Jan Kanis | 2016-04-20 09:20:47.0 | 5 |
| Ruslan Forostianov | 2015-09-09 15:04:16.0 | 3 |
| Gustavo Lopes | 2016-01-05 09:19:54.0 | 3 |
| Terry Weymouth | 2016-07-19 11:08:20.0 | 29 |
| Sijin He | 2014-05-21 14:32:04.0 | 1 |
| akhandeshi | 2014-07-29 13:10:27.0 | 14 |
| davidxn | 2013-12-16 17:55:56.0 | 27 |
| Florian Guitton | 2014-10-02 21:46:19.0 | 15 |
| Axel Oehmichen | 2014-09-04 09:33:52.0 | 2 |
| Peter Rice | 2018-01-17 10:21:31.0 | 33 |
| devjohnson | 2013-12-13 18:26:33.0 | 5 |
| Gijs Kant | 2016-03-03 08:49:08.0 | 3 |
| Hugo Berube | 2014-10-07 18:59:41.0 | 39 |
| Denny Verbeeck | 2016-07-29 13:48:05.0 | 1 |
| Hugo Berube | 2014-10-07 18:59:02.0 | 18 |
Other Committers
| User | Most Recent Commit | # Commits | |
|---|---|---|---|
| Ami Khandeshi | ami.khandeshi@pfizer.com | 2014-07-19 00:27:16.0 | 7 |
| Chris Uhrich | cuhrich@recomdata.com | 2013-11-26 18:48:33.0 | 2 |
| unknown | engina01@amrcewlr9eg45a.amer.pfizer.com | 2013-12-06 15:24:10.0 | 1 |
| unknown | engina01@amrcewlr9eg45a.amer.pfizer.com | 2013-12-06 15:24:10.0 | 1 |
| unknown | engina01@amrcvwlpk0x369.amer.pfizer.com | 2014-02-09 06:31:38.0 | 1 |
| Keith Nangle | keith.nangle@transmartfoundation.org | 2016-01-29 17:46:27.0 | 2 |
| zameershaikh | mohamshaikh@deloitte.com | 2013-12-02 10:01:22.0 | 7 |
| Parul Khullar | parul.khullar@gmail.com | 2013-11-15 10:05:42.0 | 1 |
//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