EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions
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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: | 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: | ||
# If the project is created via GPMS the database will already be set up. | |||
# In the GPMS add the use ''emma - Emma Daemon'' to your project with role ''Daemon'' | |||
# Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) | |||
Command: | |||
<code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code> | |||
# Import the Ontology information (Ontology-COMPLETE.xml) | |||
Command: | |||
<code><nowiki>test_import -p "Project" XMLFILE </nowiki></code> | |||
# Import all necessary functions (AllTools.xml) | |||
Command: | |||
<code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code> | |||
# Add the "ALL" group, if this has not already been done during the GPMS-Setup | |||
Command: | |||
<code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface | |||
# Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function) | |||
# Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk) (Don't forget to assign the imported arraylayout to the group "ALL", if you wish that all users will afterwards be able to use it!) | |||
The XML-files are currently only available in the CVS repository (Directory: CVSROOT/bioinfo/emma2/src/dbshema). | The XML-files are currently only available in the CVS repository (Directory: CVSROOT/bioinfo/emma2/src/dbshema). | ||
Revision as of 15:48, 10 October 2005
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:
- If the project is created via GPMS the database will already be set up.
- In the GPMS add the use emma - Emma Daemon to your project with role Daemon
- Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
Command:
test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE
- Import the Ontology information (Ontology-COMPLETE.xml)
Command:
test_import -p "Project" XMLFILE
- Import all necessary functions (AllTools.xml)
Command:
test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE
- 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
- Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function)
- Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk) (Don't forget to assign the imported arraylayout to the group "ALL", if you wish that all users will afterwards be able to use it!)
The XML-files are currently only available in the CVS repository (Directory: CVSROOT/bioinfo/emma2/src/dbshema).