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.

  If you are running the update procedure from a cvs directory, amke shure you have the folowing symbolic links in the directory  
   CVSDIR/bioinfo/emma2/bin 

lrwxrwxrwx    1 mdondrup bioinfo        10 Feb 18  2005 runtool_emma -> emma_start
lrwxrwxrwx    1 mdondrup bioinfo        10 Feb 22  2005 test_import -> emma_start
 

2. In the GPMS add the user emma - Emma Daemon as member 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 5 using the EMMA 2.0 web interface

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

Note: All functions have to be configured. These values will become the default values for the project.

Configure the  Writer:DBAD  function to use the appropriate QuantitationTypeDimension for your pipeline:

• CEBITEC:Spotted:[[NormalizedFeature]] for normalization-pipelines
• CEBITEC:Spotted:[[SignificanceTest]] for significance test pipelines
• CEBITEC:Spotted:[[LimmaTest]] for a LIMMA sign. test pipeline

All other Writer functions should not need further configuration.

8. Import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk) using the web-interface

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