EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions

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<!-- ## 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)]
 
  If you are running the update procedure from a cvs directory, amke shure you have the folowing symbolic links in the directory 
  <code><nowiki> CVSDIR/bioinfo/emma2/bin </nowiki></code>
<pre><nowiki>
lrwxrwxrwx    1 mdondrup bioinfo        10 Feb 18  2005 runtool_emma -> emma_start
lrwxrwxrwx    1 mdondrup bioinfo        10 Feb 22  2005 test_import -> emma_start
</nowiki></pre>
 
 
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:
<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 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 <code><nowiki> Writer:DBAD </nowiki></code> function to use the appropriate QuantitationTypeDimension for your pipeline:
 
* <code><nowiki> CEBITEC:Spotted:[[NormalizedFeature]]  </nowiki></code> for normalization-pipelines
* <code><nowiki> CEBITEC:Spotted:[[SignificanceTest]] </nowiki></code>  for significance test pipelines
* <code><nowiki> CEBITEC:Spotted:[[LimmaTest]] </nowiki></code>  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
 
{| border="1" cellpadding="2" cellspacing="0"
|  '''Group'''
|  '''Read'''
|  '''Edit'''
|  '''Reference'''
|  '''Delete'''
|  '''View permissions'''
|  '''Change permissions'''
|-
|  ALL
|  yes
|  undefined
|  yes
|  undefined
|  yes
|  undefined

Latest revision as of 07:16, 26 October 2011


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)

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