GenDBWiki/AdministratorDocumentation - Revision history

Agoesman at 15:27, 28 October 2011

2011-10-28T15:27:50Z

← Older revision		Revision as of 17:27, 28 October 2011
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	As an alternative to using GenDB via the Internet at Bielefeld University, you can also download it and install it at your location. Please read the installation requirements, installing GenDB requires extensive resources and bioinformatics skills. GenDB 2.x has a web user interface (WebUI) for most user interactions. We recommend that annotation teams use that web interface. In addition to this interface GenDB also has a Gtk-1/Gnome-1 based graphical user interface (GUI) that has some added value, but is difficult to install.		As an alternative to using GenDB via the Internet at Bielefeld University, you can also download it and install it at your location. Please read the installation requirements, installing GenDB requires extensive resources and bioinformatics skills. GenDB 2.x has a web user interface (WebUI) for most user interactions. We recommend that annotation teams use that web interface. In addition to this interface GenDB also has a Gtk-1/Gnome-1 based graphical user interface (GUI) that has some added value, but is difficult to install.

	* /DependenciesAndRequirements		* [[GenDBWiki/AdministratorDocumentation/DependenciesAndRequirements\|Dependencies and Requirements]]
	* [[/GenDBInstallation]]		* [[GenDBWiki/AdministratorDocumentation/GenDBInstallation\|GenDB Installation]]
	* [[/GenDBInstallationFAQ]]		* [[GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ\|GenDB Installation FAQ]]
	* /UpdatingFromOlderVersions		* [[GenDBWiki/AdministratorDocumentation/UpdatingFromOlderVersions\|Updating from older Versions]]

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Admin: 22 revisions

2011-10-26T06:17:02Z

22 revisions

← Older revision	Revision as of 08:17, 26 October 2011
(No difference)

imported>AlexanderGoesmann at 15:44, 25 August 2005

2005-08-25T15:44:14Z

← Older revision		Revision as of 17:44, 25 August 2005
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	* /DependenciesAndRequirements		* /DependenciesAndRequirements
	* /GenDBInstallation		* [[/GenDBInstallation]]
	* /GenDBInstallationFAQ		* [[/GenDBInstallationFAQ]]
	* /UpdatingFromOlderVersions		* /UpdatingFromOlderVersions

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	Comment: [[GlobalConfig]].pm.template was outdated		Comment: GlobalConfig.pm.template was outdated

	reconfigure_module does not work. Templates were not		reconfigure_module does not work. Templates were not

imported>AlexanderGoesmann at 17:07, 8 March 2005

2005-03-08T17:07:01Z

← Older revision		Revision as of 19:07, 8 March 2005
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	* /DependenciesAndRequirements		* /DependenciesAndRequirements
			* /GenDBInstallation
			* /GenDBInstallationFAQ
	* /UpdatingFromOlderVersions		* /UpdatingFromOlderVersions
	* /GenDBInstallation
	-----		-----

imported>BurkhardLinke at 16:14, 8 March 2005

2005-03-08T16:14:28Z

← Older revision		Revision as of 18:14, 8 March 2005
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	- GenDB setup via Common Execution Environment (CEE)		- GenDB setup via Common Execution Environment (CEE)

	~~- installation and configuration~~

	~~- Core~~

	~~- Apache~~

	~~- Gtk~~

	- installing a GenDB patch/bugfix		- installing a GenDB patch/bugfix
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	- DRMAA and scheduler issues		- DRMAA and scheduler issues

	~~- Installation~~

	----------------------		----------------------

	Installing GenDB-2.2		Installing GenDB-2.2 from CVS

	If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your '''CVSROOT''' variable properly:		If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your '''CVSROOT''' variable properly:

imported>SebastianKonietzny at 12:31, 10 February 2005

2005-02-10T12:31:32Z

← Older revision		Revision as of 14:31, 10 February 2005
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	<pre><nowiki>		<pre><nowiki>
	cd bioinfo/bridge_install		cd bioinfo/bridge_install
	install.sh /vol/gendb-2.2/		./install.sh /vol/gendb-2.2/
	</nowiki></pre>		</nowiki></pre>

imported>AlexanderGoesmann at 21:22, 8 February 2005

2005-02-08T21:22:44Z

← Older revision		Revision as of 23:22, 8 February 2005
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	<pre><nowiki>		<pre><nowiki>
	. bioinfo/seed_stuff/generate_cebitec_config > /vol/gendb-2.2/config		. bioinfo/seed_stuff/generate_cebitec_config > /vol/gendb-2.2/config
			</nowiki></pre>


			If you cannot or don't want to use the CeBiTec configuration, create an empty configuration file, e.g.:


			<pre><nowiki>
			/vol/gendb-2.2/> touch config
	</nowiki></pre>		</nowiki></pre>

imported>AlexanderGoesmann at 21:03, 8 February 2005

2005-02-08T21:03:47Z

← Older revision		Revision as of 23:03, 8 February 2005
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	Installing GenDB-2.2		Installing GenDB-2.2

	If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your CVSROOT variable properly:		If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your '''CVSROOT''' variable properly:

imported>AlexanderGoesmann at 20:59, 8 February 2005

2005-02-08T20:59:42Z

← Older revision		Revision as of 22:59, 8 February 2005
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	- Installation		- Installation

	~~Install GenDB 2.2~~		----------------------

	go to your ~~CVS bioinfo directory~~		Installing GenDB-2.2

			If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your CVSROOT variable properly:


	<pre><nowiki>		<pre><nowiki>
	~~cd ~~~/~~CVS_HEAD~~		export CVSROOT=:ext:juser@porta.Genetik.Uni-Bielefeld.DE:/vol/cvs/intern/cvsroot
	</nowiki></pre>		</nowiki></pre>


	If you ~~are installing~~ to ~~an external destination,~~ you ~~first~~ have ~~to set your CVSROOT variable properly~~		Go to a directory of your choice where you would like to install all software modules (you should have approximately 10 MB free disk space), e.g.:


	<pre><nowiki>		<pre><nowiki>
	~~export CVSROOT=:ext:juser@porta.Genetik.Uni-Bielefeld.DE:~~/vol~~/cvs/intern/cvsroot~~		cd /vol
	</nowiki></pre>		</nowiki></pre>


	Create a directory to install your local GenDB-2.2 version		Create a directory to install your local GenDB-2.2 version:


	<pre><nowiki>		<pre><nowiki>
	~~cd /vol~~
	mkdir gendb-2.2		mkdir gendb-2.2
	cd gendb-2.2		cd gendb-2.2
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	Checkout the HEAD version of the '''bridge_install''' module		Checkout the HEAD version of the '''bridge_install''' module:


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	Or update your files if you already checked out a ~~cvs~~ version		Or update your files if you have already checked out a CVS version:


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	Call the install.sh script which is located in bioinfo/bridge_install to set up the installation system. Define target directory (/vol/gendb-2.2 in this case).		Call the install.sh script which is located in bioinfo/bridge_install to set up the installation system. Define the target directory for the installation (/vol/gendb-2.2 in this case):


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	The next step is optional:		The next step is optional:
	~~call~~ the script generate_cebitec_config to generate an initial ~~configfile~~		Call the script generate_cebitec_config to generate an initial configuration file. This will produce the typical settings for SUN Grid Enginge (SGE), SQL databases and sequence databases used at CeBiTec.
	This will produce the typical settings for ~~sge~~, ~~datbases~~ and ~~biodbs~~ used at
	~~the cebitec environment~~		Please checkout the bioinfo/seed_stuff module as well:
	Please checkout the bioinfo/seed_stuff module as well

	<pre><nowiki>		<pre><nowiki>
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	go to bin directory of your installation		Go to the '''bin''' directory of your installation directory:


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	~~install~~ the modules from CVS in the following order and activate each of them		Install the modules from CVS in the following order and activate each of them
	If you want to set the configuration settings interactively via gui ommit the -c param		If you want to set the configuration settings interactively via gui ommit the -c param

imported>SebastianKonietzny at 20:42, 8 February 2005

2005-02-08T20:42:42Z

← Older revision		Revision as of 22:42, 8 February 2005
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	If you are installing on an external destination, you first have to set your CVSROOT properly		If you are installing to an external destination, you first have to set your CVSROOT variable properly