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-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 |