EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions
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1. If the project is created via GPMS the database will already be set up. | 1. If the project is created via GPMS the database will already be set up. | ||
2. In the GPMS add the | 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) | 3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) | ||
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<code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface | <code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface | ||
7. Create pipelines from the functions imported in step | 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'' | /!\ Always create a pipline with the exact name ''ArrayLayoutImport'' consisting solely of the function ''ArrayLayout Import'' | ||
8. | 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 | 9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission | ||
Revision as of 16:09, 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:
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.
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-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 |