GenDBWiki/AdministratorDocumentation/GenDBInstallation - Revision history

Agoesman at 14:40, 31 October 2011

2011-10-31T14:40:14Z

← Older revision		Revision as of 16:40, 31 October 2011
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	~~__NOTOC__~~
	= GenDB Installation Instructions =		= GenDB Installation Instructions =

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	GenDB 2.2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE!		GenDB 2.2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE!

	* 1: Checking system requirements		== Checking system requirements ==
			As a Perl application, GenDB 2.2 requires a recent version of Perl and a number of additional (non bioinformatics related) tools:
	As a Perl application, GenDB 2.2 requires a recent version of Perl and a number of additional (non bioinformatics related) tools:
	* Perl (version 5.8 or higher)		* Perl (version 5.8 or higher)
	* MySQL (version 4.0 or higher)		* MySQL (version 4.0 or higher)
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	* Apache ([http://httpd.apache.org])		* Apache ([http://httpd.apache.org])
	* mod_perl (optional, but "highly recommended" [http://perl.apache.org])		* mod_perl (optional, but "highly recommended" [http://perl.apache.org])
			You also need an administrative account at the MySQL server for creating several databases during the installation.

	~~You also need an administrative account at the MySQL server for creating several databases during the installation.~~		== Installing the required Perl modules ==
			GenDB 2.2 relies on a number of freely available Perl modules. These modules are available at the CPAN archive ([http://www.cpan.org]). You need to install these modules prior to installing GenDB 2.2. Depending on the kind of operating system these modules may also be available as packages provided by your operating system vendors; using these packages is recommended.
	* 2: Installing the required Perl modules		List of required Perl modules (in no particular order):

	GenDB 2.2 relies on a number of freely available Perl modules. These modules are available at the CPAN archive ([http://www.cpan.org]). You need to install these modules prior to installing GenDB 2.2.

	Depending on the kind of operating system these modules may also be available as packages provided by your operating system vendors; using these packages is recommended.

	List of required Perl modules (in no particular order):
	* Graph		* Graph
	* GD		* GD
Line 50:		Line 43:
	* BioPerl (also available at [http://www.bioperl.org])		* BioPerl (also available at [http://www.bioperl.org])

	Please keep in mind that these modules may have further requirements and may depend on further modules or libraries. If you are going to install the modules by yourself instead of using ready-made packages, using the so called "CPAN Shell" will help you resolving dependencies and installing modules. See the section about [http://www.cpan.org/misc/cpan-faq.html#How_install_Perl_modules installing Perl modules] at the CPAN website or the manpage of the CPAN module (if installed). Newer versions of Perl (> 5.8) also provide an improved version of the CPAN Shell, called "CPANPlus".		Please keep in mind that these modules may have further requirements and may depend on further modules or libraries. If you are going to install the modules by yourself instead of using ready-made packages, using the so called "CPAN Shell" will help you resolving dependencies and installing modules. See the section about [http://www.cpan.org/misc/cpan-faq.html#How_install_Perl_modules installing Perl modules] at the CPAN website or the manpage of the CPAN module (if installed). Newer versions of Perl (> 5.8) also provide an improved version of the CPAN Shell, called "CPANPlus".
	* 3: Installing bioinformatics software

	~~GenDB 2.2 does not contain methods for gene calling or predicting gene functions; it uses a number of mostly freely available, well-known tools. Most of these tools are required for running GenDB 2.2~~.

			== Installing bioinformatics software ==
			GenDB 2.2 does not contain methods for gene calling or predicting gene functions; it uses a number of mostly freely available, well-known tools. Most of these tools are required for running GenDB 2.2.
	* Gene calling:		* Gene calling:
	** Critica		** Critica
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	** TMHMM (optional)		** TMHMM (optional)
	** SignalP (optional)		** SignalP (optional)
	~~<br>~~
	~~At least the mandatory tools need to be setup and configured properly.~~

	* 4: Getting the required sequence databases

	~~The~~ tools ~~described above operate on various databases containing biological sequences, pattern, HMMs etc. You~~ need ~~at least the following databases for GenDB 2~~.2:		At least the mandatory tools need to be setup and configured properly.

			== Getting the required sequence databases ==
			The tools described above operate on various databases containing biological sequences, pattern, HMMs etc. You need at least the following databases for GenDB 2.2:
	* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)		* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)
	* a non redundant protein database ("nr", also available at the NCBI/EBI)		* a non redundant protein database ("nr", also available at the NCBI/EBI)
	* a blastable SwissProt database		* a blastable SwissProt database<br>You may either use a standalone database or a subset of the "nr" database provided by the NCBI or the EBI. Setting up this subset is beyond the scope of this documentation.
	You may either use a standalone database or a subset of the "nr" database provided by the NCBI or the EBI. Setting up this subset is beyond the scope of this documentation.		* a database containing the protein sequences of all genomes available in the KeGG database<br>You can build this database by downloading the sequences from the KeGG [ftp://ftp.genome.jp/pub/kegg/genomes/sequences ftp server] and concatenating the necessary files.
	* a database containing the protein sequences of all genomes available in the KeGG database
	You can build this database by downloading the sequences from the KeGG [ftp://ftp.genome.jp/pub/kegg/genomes/sequences ftp server] and concatenating the necessary files.

	You have to ensure that the ~~fasta~~ header line format follows the defline format required by the NCBI. See the documentation to "formatdb" and "fastacmd" and [ftp://ftp.ncbi.nih.gov/blast/db/README]. If you want to use custom databases within GenDB, the header lines also have to follow the defline standard.		You have to ensure that the FASTA header line format follows the defline format required by the NCBI. See the documentation to "formatdb" and "fastacmd" and [ftp://ftp.ncbi.nih.gov/blast/db/README]. If you want to use custom databases within GenDB, the header lines also have to follow the defline standard.

	* ~~5: Getting~~ the most recent GenDB tarball from sourceforge([http://sourceforge.net/projects/gendb])		== Installing GenDB ==
	* ~~6: Unpacking~~ the tarball in a temporary directory		* Get the most recent GenDB tarball from sourceforge([http://sourceforge.net/projects/gendb])
	* 7: Run the installation script ("sh install_gendb.sh <target directory>")		* Unpack the tarball in a temporary directory
			* Run the installation script ("sh install_gendb.sh <target directory>")

	The installation script will check for the Perl modules, paths to binaries and databases, install the components and setup the system.		The installation script will check for the Perl modules, paths to binaries and databases, install the components and setup the system.

	Note:		Note:
	* The GOPArc component downloads several databases from external servers, like the COG and KOG databases and the KeGG databases (others than the database mentioned above). You need an internet connection during the installation. The installation script will ask for a proxy server to be used for downloading. If you do not need a proxy leave the field empty. Otherwise enter the complete proxy URL, e.g. `http://proxy.my-institute.org:1234`.		* The GOPArc component downloads several databases from external servers, like the COG and KOG databases and the KeGG databases (others than the database mentioned above). You need an internet connection during the installation. The installation script will ask for a proxy server to be used for downloading. If you do not need a proxy leave the field empty. Otherwise enter the complete proxy URL, e.g. `http://proxy.my-institute.org:1234`.
	* During download the script also tries to fetch the KeGG pathway reference maps. These are about 2.300 single files, which unfortunatly have to be fetched one by one.		* During download the script also tries to fetch the KeGG pathway reference maps. These are about 2.300 single files, which unfortunatly have to be fetched one by one.
	* Some of the installation scripts produce a lot of output with warnings and error messages. We are aware of this and will fix it in the next release.		* Some of the installation scripts produce a lot of output with warnings and error messages. We are aware of this and will fix it in the next release.
	* 8: Setting up the web server

	The apache web server is usually available as a package provided by the operating system vendors; however the way to configure the server differs between operating systems and distributions. We have provided a script called "setup_web_interface" that tries to detect the apache version and is able to create a configuration fragment you can use to setup the web server. The fragment contains the necessary configuration directives, but may need to be adopted to your local installation.		== Setting up the web server ==

			The apache web server is usually available as a package provided by the operating system vendors; however the way to configure the server differs between operating systems and distributions. We have provided a script called "setup_web_interface" that tries to detect the apache version and is able to create a configuration fragment you can use to setup the web server. The fragment contains the necessary configuration directives, but may need to be adopted to your local installation.

	* 9: Start a dispatcher		== Starting the dispatcher ==

	The "dispatcher" is the part of GenDB 2.2 responsible for managing external tools, running them on the cluster, parsing output and so on. It needs to be started prior to submitting tools within the GenDB 2.2 web interface or by a command line script. Starting a dispatcher is simple:		The "dispatcher" is the part of GenDB 2.2 responsible for managing external tools, running them on the cluster, parsing output and so on. It needs to be started prior to submitting tools within the GenDB 2.2 web interface or by a command line script. Starting a dispatcher is simple:

	* `cd` into the `/bin` directory of your GenDB installation		* `cd` into the `/bin` directory of your GenDB installation
Line 108:		Line 98:
	* for advanced options just execute `./dispatcher` without any arguments		* for advanced options just execute `./dispatcher` without any arguments

	You may start the dispatcher at system boot time, using a so called "init script". Again these scripts differ between operating systems and distributions, so we are not able to provide a ready-made one. Ask your local system administrator for more information about how to write an init script.		You may start the dispatcher at system boot time, using a so called "init script". Again these scripts differ between operating systems and distributions, so we are not able to provide a ready-made one. Ask your local system administrator for more information about how to write an init script.

	The installation is finished now and you can start with adding a new GenDB project and processing the first data. See [[GenDBWiki/CoreDocumentation/CoreScripts\|the core scripts page]] for more information about this.		The installation is finished now and you can start with adding a new GenDB project and processing the first data. See [[GenDBWiki/CoreDocumentation/CoreScripts\|the core scripts page]] for more information about this.

Admin: 24 revisions

2011-10-26T06:14:33Z

24 revisions

← Older revision	Revision as of 08:14, 26 October 2011
(No difference)

imported>AlexanderGoesmann at 16:16, 15 December 2005

2005-12-15T16:16:00Z

← Older revision		Revision as of 18:16, 15 December 2005
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	* 1: Checking system requirements		* 1: Checking system requirements
	As a Perl application, GenDB 2.2 requires a recent version of Perl and a number of additional (non bioinformatics related) tools:
			As a Perl application, GenDB 2.2 requires a recent version of Perl and a number of additional (non bioinformatics related) tools:
	* Perl (version 5.8 or higher)		* Perl (version 5.8 or higher)
	* MySQL (version 4.0 or higher)		* MySQL (version 4.0 or higher)
Line 21:		Line 22:
	* mod_perl (optional, but "highly recommended" [http://perl.apache.org])		* mod_perl (optional, but "highly recommended" [http://perl.apache.org])

	You also need an administrative account at the MySQL server for creating several databases during the installation.		You also need an administrative account at the MySQL server for creating several databases during the installation.

	* 2: Installing the required Perl modules		* 2: Installing the required Perl modules
	~~GenDB 2.2 relies on a number of freely available Perl modules. These modules are available at the CPAN archive ([http://www.cpan.org]). You need to install these modules prior to installing GenDB 2.2.~~

	~~Depending~~ on ~~the kind~~ of ~~operating system these~~ modules ~~may also be~~ available ~~as packages provided by your operating system vendors; using~~ these ~~packages is recommended~~.		GenDB 2.2 relies on a number of freely available Perl modules. These modules are available at the CPAN archive ([http://www.cpan.org]). You need to install these modules prior to installing GenDB 2.2.

	List of required Perl modules (in no particular order):		Depending on the kind of operating system these modules may also be available as packages provided by your operating system vendors; using these packages is recommended.

			List of required Perl modules (in no particular order):
	* Graph		* Graph
	* GD		* GD
Line 48:		Line 50:
	* BioPerl (also available at [http://www.bioperl.org])		* BioPerl (also available at [http://www.bioperl.org])

	Please keep in mind that these modules may have further requirements and may depend on further modules or libraries. If you are going to install the modules by yourself instead of using ready-made packages, using the so called "CPAN Shell" will help you resolving dependencies and installing modules. See the section about [http://www.cpan.org/misc/cpan-faq.html#How_install_Perl_modules installing Perl modules] at the CPAN website or the manpage of the CPAN module (if installed). Newer versions of Perl (> 5.8) also provide an improved version of the CPAN Shell, called "CPANPlus".		Please keep in mind that these modules may have further requirements and may depend on further modules or libraries. If you are going to install the modules by yourself instead of using ready-made packages, using the so called "CPAN Shell" will help you resolving dependencies and installing modules. See the section about [http://www.cpan.org/misc/cpan-faq.html#How_install_Perl_modules installing Perl modules] at the CPAN website or the manpage of the CPAN module (if installed). Newer versions of Perl (> 5.8) also provide an improved version of the CPAN Shell, called "CPANPlus".
	* 3: Installing bioinformatics software		* 3: Installing bioinformatics software
	GenDB 2.2 does not contain methods for gene calling or predicting gene functions; it uses a number of mostly freely available, well-known tools. Most of these tools are required for running GenDB 2.2.
			GenDB 2.2 does not contain methods for gene calling or predicting gene functions; it uses a number of mostly freely available, well-known tools. Most of these tools are required for running GenDB 2.2.

	* Gene calling:		* Gene calling:
Line 71:		Line 74:

	* 4: Getting the required sequence databases		* 4: Getting the required sequence databases
	The tools described above operate on various databases containing biological sequences, pattern, HMMs etc. You need at least the following databases for GenDB 2.2:
			The tools described above operate on various databases containing biological sequences, pattern, HMMs etc. You need at least the following databases for GenDB 2.2:

	* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)		* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)
Line 85:		Line 89:
	* 6: Unpacking the tarball in a temporary directory		* 6: Unpacking the tarball in a temporary directory
	* 7: Run the installation script ("sh install_gendb.sh <target directory>")		* 7: Run the installation script ("sh install_gendb.sh <target directory>")
	The installation script will check for the Perl modules, paths to binaries and databases, install the components and setup the system.
			The installation script will check for the Perl modules, paths to binaries and databases, install the components and setup the system.

	Note:		Note:
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	* Some of the installation scripts produce a lot of output with warnings and error messages. We are aware of this and will fix it in the next release.		* Some of the installation scripts produce a lot of output with warnings and error messages. We are aware of this and will fix it in the next release.
	* 8: Setting up the web server		* 8: Setting up the web server
	The apache web server is usually available as a package provided by the operating system vendors; however the way to configure the server differs between operating systems and distributions. We have provided a script called "setup_web_interface" that tries to detect the apache version and is able to create a configuration fragment you can use to setup the web server. The fragment contains the necessary configuration directives, but may need to be adopted to your local installation.
			The apache web server is usually available as a package provided by the operating system vendors; however the way to configure the server differs between operating systems and distributions. We have provided a script called "setup_web_interface" that tries to detect the apache version and is able to create a configuration fragment you can use to setup the web server. The fragment contains the necessary configuration directives, but may need to be adopted to your local installation.

	* 9: Start a dispatcher		* 9: Start a dispatcher
	The "dispatcher" is the part of GenDB 2.2 responsible for managing external tools, running them on the cluster, parsing output and so on. It needs to be started prior to submitting tools within the GenDB 2.2 web interface or by a command line script. You may start the dispatcher at system boot time, using a so called "init script". Again these scripts differ between operating systems and distributions, so we are not able to provide a ready-made one. Ask your local system administrator for more information about how to write an init script.
			The "dispatcher" is the part of GenDB 2.2 responsible for managing external tools, running them on the cluster, parsing output and so on. It needs to be started prior to submitting tools within the GenDB 2.2 web interface or by a command line script. Starting a dispatcher is simple:

			* `cd` into the `/bin` directory of your GenDB installation
			* execute `./dispatcher -l /tmp/your_dispatcher.log`
			* for advanced options just execute `./dispatcher` without any arguments

			You may start the dispatcher at system boot time, using a so called "init script". Again these scripts differ between operating systems and distributions, so we are not able to provide a ready-made one. Ask your local system administrator for more information about how to write an init script.

	The installation is finished now and you can start with adding a new GenDB project and processing the first data. See [[GenDBWiki/CoreDocumentation/CoreScripts\|the core scripts page]] for more information about this.		The installation is finished now and you can start with adding a new GenDB project and processing the first data. See [[GenDBWiki/CoreDocumentation/CoreScripts\|the core scripts page]] for more information about this.

imported>FolkerMeyer at 14:33, 19 October 2005

2005-10-19T14:33:40Z

← Older revision		Revision as of 16:33, 19 October 2005
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	You have to ensure that the fasta header line format follows the defline format required by the NCBI. See the documentation to "formatdb" and "fastacmd" and [ftp://ftp.ncbi.nih.gov/blast/db/README]. If you want to use custom databases within GenDB, the header lines also have to follow the defline standard.		You have to ensure that the fasta header line format follows the defline format required by the NCBI. See the documentation to "formatdb" and "fastacmd" and [ftp://ftp.ncbi.nih.gov/blast/db/README]. If you want to use custom databases within GenDB, the header lines also have to follow the defline standard.

	* 5: Getting the GenDB ~~2.2~~ tarball ([~~ftp~~://~~ftp.cebitec.uni-bielefeld~~.~~de/pub~~/~~software~~/gendb])		* 5: Getting the most recent GenDB tarball from sourceforge([http://sourceforge.net/projects/gendb])
	* 6: Unpacking the tarball in a temporary directory		* 6: Unpacking the tarball in a temporary directory
	* 7: Run the installation script ("sh install_gendb.sh <target directory>")		* 7: Run the installation script ("sh install_gendb.sh <target directory>")

imported>AlexanderGoesmann at 14:55, 29 August 2005

2005-08-29T14:55:00Z

← Older revision		Revision as of 16:55, 29 August 2005
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	Below you can find some basic installation instructions for installing GenDB from a tarball. There's also a [[GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ\|FAQ page]] describing some of the problems that may occur during installation.		Below you can find some basic installation instructions for installing GenDB from a tarball. There's also a [[GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ\|FAQ page]] describing some of the problems that may occur during installation.

	~~/!\ Be aware that the current version of GenDB 2.2 is a '''release candidate'''. /!\~~

	Although we are testing our software on a number of systems prior to release, it may contain errors and in the worst case it does not work in the way you expect it.		Although we are testing our software on a number of systems prior to release, it may contain errors and in the worst case it does not work in the way you expect it.

imported>AlexanderGoesmann at 14:21, 25 August 2005

2005-08-25T14:21:21Z

← Older revision		Revision as of 16:21, 25 August 2005
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	* 4: Getting the required sequence databases		* 4: Getting the required sequence databases
	The tools described above operate on various databases containing biological sequences, pattern, HMMs etc. You need at least the following databases for GenDB 2,2:		The tools described above operate on various databases containing biological sequences, pattern, HMMs etc. You need at least the following databases for GenDB 2.2:

	* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)		* a non redundant nucleotide database (usually called "nt", available by ftp at the NCBI and the EBI)

Unknown user at 12:45, 22 August 2005

2005-08-22T12:45:24Z

← Older revision		Revision as of 14:45, 22 August 2005
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	__NOTOC__		__NOTOC__
	= GenDB Installation Instructions =		= GenDB Installation Instructions =

	~~TestTEXT mit !~~

	~~TestTEXT mit~~

	Below you can find some basic installation instructions for installing GenDB from a tarball. There's also a [[GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ\|FAQ page]] describing some of the problems that may occur during installation.		Below you can find some basic installation instructions for installing GenDB from a tarball. There's also a [[GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ\|FAQ page]] describing some of the problems that may occur during installation.

Unknown user at 12:42, 22 August 2005

2005-08-22T12:42:27Z

← Older revision		Revision as of 14:42, 22 August 2005
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	__NOTOC__		__NOTOC__
	= GenDB Installation Instructions =		= GenDB Installation Instructions =

	~~[[TestText]] ohne !~~

	~~TestText mit !~~

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	TestTEXT mit !		TestTEXT mit !

Unknown user at 12:41, 22 August 2005

2005-08-22T12:41:55Z

← Older revision		Revision as of 14:41, 22 August 2005
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	= GenDB Installation Instructions =		= GenDB Installation Instructions =

	[[TestText]]		[[TestText]] ohne !

	TestText mit !		TestText mit !

	TestTEXT ohne		TestTEXT ohne !

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Unknown user at 12:40, 22 August 2005

2005-08-22T12:40:23Z

← Older revision		Revision as of 14:40, 22 August 2005
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	TestText mit !		TestText mit !

			TestTEXT ohne

	TestTEXT mit !		TestTEXT mit !