NOTE: We are working on migrating this site away from MediaWiki, so editing pages will be disabled for now.
Difference between revisions of "XORT Dumper HOWTO"
(Added initial structure for the XORT dumping HOWTO.) |
(Added info on setting up server and installing XORT.) |
||
| Line 6: | Line 6: | ||
| − | '''THIS IS A WORK IN PROGRESS''' | + | '''THIS IS A WORK IN PROGRESS. IT IS NOT FINISHED!''' |
==Authors== | ==Authors== | ||
| Line 13: | Line 13: | ||
==Prerequisites== | ==Prerequisites== | ||
| + | The steps outlined in this HOWTO were done using Ubuntu server 7.10. It is assumed that you have this type of server setup and configued with the following. | ||
| − | * | + | * PostgreSQL |
* Perl | * Perl | ||
| − | |||
| − | |||
| + | ==System Setup== | ||
| + | 1. Install make, gcc, autoconf, automake, and binutils. | ||
| + | > sudo apt-get install make gcc autoconf automake binutils | ||
| + | 2. Install Perl libraries | ||
| + | > sudo apt-get install libxml-perl libxml-dom-perl libxml-sax-perl | ||
| + | > sudo apt-get install libdbi-perl libdbd-pg-perl | ||
| + | ==Chado Database Setup== | ||
| + | 1. Create a PostgreSQL database user | ||
| + | > sudo su - postgres | ||
| + | postgres> createuser | ||
| + | Then follow the prompts to create a user that has permission to create databases. Once done exit the postgres user account. | ||
| + | |||
| + | 2. Fetch the SGDlite Chado dump | ||
| + | > wget http://yfgdb.princeton.edu/download/sgdlite/sgdlite.sql.gz | ||
| + | |||
| + | 3. Create and load the SGDlite database | ||
| + | > createdb sgdlite | ||
| + | > zcat sgdlite.sql.gz | psql -d sgdlite -o sgdlite_load.log | ||
| + | |||
| + | ==XORT Installation== | ||
| + | |||
| + | > wget http://superb-west.dl.sourceforge.net/sourceforge/gmod/XML-XORT-0.008.tar.gz | ||
| + | > tar zxf XML-XORT-0.008.tar.gz | ||
| + | > cd XML-XORT-0.008 | ||
| + | > perl Makefile.PL | ||
| + | What is the database name? sgdlite | ||
| + | What is the database username? jogoodma | ||
| + | What is the password for 'jogoodma'? <enter> - none specified | ||
| + | What is the database host? localhost | ||
| + | What is your database port? 5432 | ||
| + | Where will the tmp directory go? /tmp | ||
| + | Where will the conf directory go? /usr/local/xort/conf | ||
| + | Where is the DDL file? <enter> - accept default | ||
| + | Where do you want to install XORT if other than default, press ENTER if default: <enter> | ||
| + | > make | ||
| + | > sudo make install | ||
| + | |||
| + | ==Dumping Genes== | ||
Revision as of 18:12, 12 November 2007
Contents
Introduction
This HOWTO describes a method for dumping data from Chado into Chado XML using XORT.
THIS IS A WORK IN PROGRESS. IT IS NOT FINISHED!
Authors
Prerequisites
The steps outlined in this HOWTO were done using Ubuntu server 7.10. It is assumed that you have this type of server setup and configued with the following.
- PostgreSQL
- Perl
System Setup
1. Install make, gcc, autoconf, automake, and binutils.
> sudo apt-get install make gcc autoconf automake binutils
2. Install Perl libraries
> sudo apt-get install libxml-perl libxml-dom-perl libxml-sax-perl > sudo apt-get install libdbi-perl libdbd-pg-perl
Chado Database Setup
1. Create a PostgreSQL database user
> sudo su - postgres postgres> createuser
Then follow the prompts to create a user that has permission to create databases. Once done exit the postgres user account.
2. Fetch the SGDlite Chado dump
> wget http://yfgdb.princeton.edu/download/sgdlite/sgdlite.sql.gz
3. Create and load the SGDlite database
> createdb sgdlite > zcat sgdlite.sql.gz | psql -d sgdlite -o sgdlite_load.log
XORT Installation
> wget http://superb-west.dl.sourceforge.net/sourceforge/gmod/XML-XORT-0.008.tar.gz > tar zxf XML-XORT-0.008.tar.gz > cd XML-XORT-0.008 > perl Makefile.PL What is the database name? sgdlite What is the database username? jogoodma What is the password for 'jogoodma'? <enter> - none specified What is the database host? localhost What is your database port? 5432 Where will the tmp directory go? /tmp Where will the conf directory go? /usr/local/xort/conf Where is the DDL file? <enter> - accept default Where do you want to install XORT if other than default, press ENTER if default: <enter> > make > sudo make install
Dumping Genes
More Information
See the XORT page.
Please send questions to the GMOD developers list:
gmod-devel@lists.sourceforge.net
Or contact the GMOD Help Desk
