EMMAWiki/AdministratorDocumentation/ProjectSetup

Project Setup

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, make sure 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 Command:

 gpms add_member -l emma -p "Project" -r deamon 

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 

Uncheck the Save as template option when saving the pipeline. otherwise it will show up in the analyze array page

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

Project Setup via Database Dump

1. Export the desired project by:

mysqldump -p -h dbhost -P 3306 [source database name] > my_project_dump.sql

2. After that import it into the target database:

mysql -p [target database name] < my_project_dump.sql

3. In the GPMS add the user emma - Emma Daemon as member to your project with role Daemon. See above for the command.

4. Add the "ALL" group, if this has not already been done during the GPMS-Setup. See above for the command.