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, 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
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-pipelinesCEBITEC:Spotted:[[SignificanceTest]]for significance test pipelinesCEBITEC: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 |