EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions

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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)]
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)]
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.
  If you are running the update procedure from a cvs directory, make sure 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>
<span id="addEmmaDaemon"></span>
2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''
Command:
<code><nowiki> gpms add_member -l emma -p "Project" -r deamon </nowiki></code>
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>
<span id="addAllGroup"></span>
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''
Uncheck the ''Save as template'' option when saving the pipeline. otherwise it will show up in the ''analyze array'' page
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
|}
== Project Setup via Database Dump ==
1. Export the desired project by:
<pre><nowiki>
mysqldump -p -h dbhost -P 3306 [source database name] > my_project_dump.sql
</nowiki></pre>
2. After that import it into the target database:
<pre><nowiki>
mysql -p [target database name] < my_project_dump.sql
</nowiki></pre>
3. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''. [[#addEmmaDaemon|See above for the command]].
4. Add the "ALL" group, if this has not already been done during the GPMS-Setup. [[#addAllGroup|See above for the command]].

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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