EMMAWiki/AdministratorDocumentation/ProjectSetup - Revision history

Admin: 17 revisions

2011-10-26T06:16:37Z

17 revisions

← Older revision	Revision as of 08:16, 26 October 2011
(No difference)

imported>KaiRunte at 08:36, 11 October 2005

2005-10-11T08:36:31Z

← Older revision		Revision as of 10:36, 11 October 2005
Line 5:		Line 5:

	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]].~~

imported>KaiRunte at 08:35, 11 October 2005

2005-10-11T08:35:56Z

← Older revision		Revision as of 10:35, 11 October 2005
Line 3:		Line 3:

	= Project Setup =		= Project Setup =

			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:		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:

imported>KaiRunte at 08:26, 11 October 2005

2005-10-11T08:26:32Z

← Older revision		Revision as of 10:26, 11 October 2005
Line 20:		Line 20:


			<span id="addEmmaDaemon"></span>
	2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''		2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''
	Command:		Command:
Line 36:		Line 37:
	<code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>		<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		6. Add the "ALL" group, if this has not already been done during the GPMS-Setup
	Command:		Command:
Line 92:		Line 94:


	3. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''. See above for the command.		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. 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]].

imported>KaiRunte at 08:24, 11 October 2005

2005-10-11T08:24:20Z

← Older revision		Revision as of 10:24, 11 October 2005
Line 90:		Line 90:
	mysql -p [target database name] < my_project_dump.sql		mysql -p [target database name] < my_project_dump.sql
	</nowiki></pre>		</nowiki></pre>


			3. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''. See above for the command.

			4. Add the "ALL" group, if this has not already been done during the GPMS-Setup. See above for the command.

imported>KaiRunte at 08:21, 11 October 2005

2005-10-11T08:21:21Z

← Older revision		Revision as of 10:21, 11 October 2005
Line 21:		Line 21:

	2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''		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)		3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)

imported>KaiRunte at 16:52, 10 October 2005

2005-10-10T16:52:42Z

← Older revision		Revision as of 18:52, 10 October 2005
Line 77:		Line 77:

	1. Export the desired project by:		1. Export the desired project by:
	<~~code~~><nowiki> mysqldump -p -h dbhost -P 3306 [source database name] > my_project_dump.sql </nowiki></~~code~~>
			<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:		2. After that import it into the target database:
	~~TODO~~
			<pre><nowiki>
			mysql -p [target database name] < my_project_dump.sql
			</nowiki></pre>

imported>KaiRunte at 16:50, 10 October 2005

2005-10-10T16:50:14Z

@@ Line 1: / Line 1: @@
 __NOTOC__
 <!-- ## 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:
@@ Line 68: / Line 71: @@
 |  undefined
 |  yes
 |  undefined

imported>MichaelDondrup at 15:34, 10 October 2005

2005-10-10T15:34:45Z

← Older revision		Revision as of 17:34, 10 October 2005
Line 8:		Line 8:
	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.

	If you are running the update procedure from a cvs directory, ~~amke shure~~ you have the folowing symbolic links in the directory		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>		<code><nowiki> CVSDIR/bioinfo/emma2/bin </nowiki></code>

Line 37:		Line 37:
	7. Create pipelines from the functions imported in step 5 using 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''		/!\ 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.		Note: All functions have to be configured. These values will become the default values for the project.

imported>MichaelDondrup at 15:21, 10 October 2005

2005-10-10T15:21:39Z

← Older revision		Revision as of 17:21, 10 October 2005
Line 7:		Line 7:

	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.

			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''		2. In the GPMS add the user ''emma - Emma Daemon'' as member to your project with role ''Daemon''