EMMAWiki/AdministratorDocumentation/ProjectSetup

An EMMA 2.0 Project consists of a database and a corresponding user and group management, which is supplied by the GPMS-Project Management. The database uses the MAGE-OM object description scheme. After setting up a new project as it is described in the GPMS-Documentation, this database has to be "build up", attending the following steps:

Locate the xml-files needed for the setup: The XML-files are currently in the CVS repository (Directory: CVSDIR/bioinfo/emma2/src/dbshema).

1. If the project is created via GPMS the database will already be set up.

2. In the GPMS add the use emma - Emma Daemon to your project with role Daemon

3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) Command:

 test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE 

4. Import the Ontology information (Ontology-COMPLETE.xml) Command:

test_import -p "Project" XMLFILE 

5. Import all necessary functions (AllTools.xml) Command:

 test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE 

6. Add the "ALL" group, if this has not already been done during the GPMS-Setup Command:

 emma_start add_group -g ALL  or use the EMMA 2.0 web interface

7. Create pipelines from the functions imported in step 6 using the EMMA 2.0 web interface

/!\ Always create a pipline with the exact name  ArrayLayoutImport consisting solely of the function ArrayLayout Import 

8. Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk)

9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission

Group	Read	Edit	Reference	Delete	View permissions	Change permissions
ALL	yes	undefined	yes	undefined	yes	undefined