EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions
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2.) Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) | 2.) Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) | ||
(Command: test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE) | (Command: <code><nowiki>test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE</nowiki></code>) | ||
3.) Import the Ontology information (Ontology-COMPLETE.xml) | 3.) Import the Ontology information (Ontology-COMPLETE.xml) | ||
(Command: test_import -p "Project" XMLFILE) | (Command: <code><nowiki>test_import -p "Project" XMLFILE</nowiki></code>) | ||
4.) Import all necessary functions (AllTools.xml) | 4.) Import all necessary functions (AllTools.xml) | ||
(Command: test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE) | (Command: <code><nowiki>test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE</nowiki></code>) | ||
5.) Add the "ALL" group, if this has not already been done during the GPMS-Setup | 5.) Add the "ALL" group, if this has not already been done during the GPMS-Setup | ||
(Command: emma_start add_group -g ALL) | (Command: <code><nowiki>emma_start add_group -g ALL</nowiki></code>) | ||
6.) Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function) | 6.) Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function) | ||
Revision as of 15:07, 21 September 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:
1.) If the project is created via GPMS the database will already be set up.
2.) Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
(Command: test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE)
3.) Import the Ontology information (Ontology-COMPLETE.xml)
(Command: test_import -p "Project" XMLFILE)
4.) Import all necessary functions (AllTools.xml)
(Command: test_import -p "Project" -i [[IdentifierRefAction]]=Reference,[[IdentifierClashAction]]=Update XMLFILE)
5.) Add the "ALL" group, if this has not already been done during the GPMS-Setup
(Command: emma_start add_group -g ALL)
6.) Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function)
7.) 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).