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| = Project Setup = | | = Project Setup = |
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| 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:
| | 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)] |
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| Locate the xml-files needed for the setup:
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| The XML-files are currently in the CVS repository (Directory: '''CVSDIR/bioinfo/emma2/src/dbshema''').
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| 1. If the project is created via GPMS the database will already be set up.
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| If you are running the update procedure from a cvs directory, make sure you have the folowing symbolic links in the directory
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| <code><nowiki> CVSDIR/bioinfo/emma2/bin </nowiki></code>
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| <pre><nowiki>
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| lrwxrwxrwx 1 mdondrup bioinfo 10 Feb 18 2005 runtool_emma -> emma_start
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| lrwxrwxrwx 1 mdondrup bioinfo 10 Feb 22 2005 test_import -> emma_start
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| </nowiki></pre>
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| 2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''
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| Command:
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| <code><nowiki> gpms add_member -l emma -p "Project" -r deamon </nowiki></code>
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| 3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
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| Command:
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| <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
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| 4. Import the Ontology information (Ontology-COMPLETE.xml)
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| Command:
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| <code><nowiki>test_import -p "Project" XMLFILE </nowiki></code>
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| 5. Import all necessary functions (AllTools.xml)
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| Command:
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| <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
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| 6. Add the "ALL" group, if this has not already been done during the GPMS-Setup
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| Command:
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| <code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface
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| 7. Create pipelines from the functions imported in step 5 using the EMMA 2.0 web interface
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| /!\ Always create a pipline with the exact name ''ArrayLayoutImport'' consisting solely of the function ''ArrayLayout Import''
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| Uncheck the ''Save as template'' option when saving the pipeline. otherwise it will show up in the ''analyze array'' page
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| Note: All functions have to be configured. These values will become the default values for the project.
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| Configure the <code><nowiki> Writer:DBAD </nowiki></code> function to use the appropriate QuantitationTypeDimension for your pipeline:
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| * <code><nowiki> CEBITEC:Spotted:[[NormalizedFeature]] </nowiki></code> for normalization-pipelines
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| * <code><nowiki> CEBITEC:Spotted:[[SignificanceTest]] </nowiki></code> for significance test pipelines
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| * <code><nowiki> CEBITEC:Spotted:[[LimmaTest]] </nowiki></code> for a LIMMA sign. test pipeline
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| All other Writer functions should not need further configuration.
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| 8. Import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk) using the web-interface
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| 9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission
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| {| border="1" cellpadding="2" cellspacing="0"
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| | '''Group'''
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| | '''Read'''
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| | '''Edit'''
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| | '''Reference'''
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| | '''Delete'''
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| | '''View permissions'''
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| | '''Change permissions'''
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| |-
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| | ALL
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| | yes
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| | undefined
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| | yes
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| | undefined
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| | yes
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| | undefined
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| |}
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| == Project Setup via Database Dump ==
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| 1. Export the desired project by:
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| <pre><nowiki>
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| mysqldump -p -h dbhost -P 3306 [source database name] > my_project_dump.sql
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| </nowiki></pre>
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| 2. After that import it into the target database:
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| <pre><nowiki>
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| mysql -p [target database name] < my_project_dump.sql
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| </nowiki></pre>
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| 3. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''. See above for the command.
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| 4. Add the "ALL" group, if this has not already been done during the GPMS-Setup. See above for the command.
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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)