|
|
| (11 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| __NOTOC__ | | __NOTOC__ |
| <!-- ## page was renamed from [[ProjectSetup]] --> | | <!-- ## page was renamed from [[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:
| | = Project 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.
| | So far, only a setup procedure valid for the [[CeBiTec]] installation of EMMA exists. You can find this documentation at [http://www.cebitec.uni-bielefeld.de/groups/brf/internal/AdminInfoEMMA#setup Project setup (internal)] |
| | |
| 2. In the GPMS add the use ''emma - Emma Daemon'' to your project with role ''Daemon''
| |
| | |
| 3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
| |
| Command:
| |
| <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
| |
| | |
| 4. Import the Ontology information (Ontology-COMPLETE.xml)
| |
| Command:
| |
| <code><nowiki>test_import -p "Project" XMLFILE </nowiki></code>
| |
| | |
| 5. Import all necessary functions (AllTools.xml)
| |
| Command:
| |
| <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
| |
| | |
| 6. 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
| |
| | |
| 7. Create pipelines from the functions imported in step 6 using the EMMA 2.0 web interface
| |
| /!\ Always create a pipline with the exact name ''ArrayLayoutImport'' consisting solely of the function ''ArrayLayout Import''
| |
| | |
| 8. Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk)
| |
| | |
| 9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission
| |
| | |
| {| border="1" cellpadding="2" cellspacing="0"
| |
| | '''Group'''
| |
| | '''Read'''
| |
| | '''Edit'''
| |
| | '''Reference'''
| |
| | '''Delete'''
| |
| | '''View permissions'''
| |
| | '''Change permissions'''
| |
| |-
| |
| | ALL
| |
| | yes
| |
| | undefined
| |
| | yes
| |
| | undefined
| |
| | yes
| |
| | undefined
| |
Project Setup
So far, only a setup procedure valid for the CeBiTec installation of EMMA exists. You can find this documentation at Project setup (internal)