Difference between revisions of "Website:WormMine"
From WormBaseWiki
Jump to navigationJump to search| Line 23: | Line 23: | ||
Set up postgres users and create a database: | Set up postgres users and create a database: | ||
| + | |||
| + | TH: THIS IS A HACK. I don't fully grok postgres' authentication config. | ||
<pre> | <pre> | ||
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Type "help" for help. | Type "help" for help. | ||
| − | template1=# CREATE USER intermine WITH PASSWORD ' | + | template1=# CREATE USER intermine WITH PASSWORD 'xxxxxxx'; |
CREATE ROLE | CREATE ROLE | ||
template1=# create database wormmine; | template1=# create database wormmine; | ||
| + | template1=# create database items-wormmine; | ||
CREATE DATABASE | CREATE DATABASE | ||
template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; | template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; | ||
| − | GRANT | + | template1=# GRANT ALL PRIVILEGES ON DATABASE items-wormmine to intermine; |
| − | template1=# | + | template1=# \q |
</pre> | </pre> | ||
Revision as of 15:25, 14 October 2011
Contents
Background
Based on the Getting Started Tutorial:
http://intermine.org/wiki/GettingStarted
Users and Groups
sudo adduser intermine // will be the user connecting to the mine database sudo passwd intermine xxxxxx
Install Prerequisites (Debian)
(see http://intermine.org/wiki/Prerequisites)
$ sudo apt-get install sun-java6-sdk $ sudo apt-get install ant
Postgres
$ sudo apt-get install postgresql
Set up postgres users and create a database:
TH: THIS IS A HACK. I don't fully grok postgres' authentication config.
[tharris@wb-dev: bin]> sudo -u postgres psql -d template1 -U postgres psql (8.4.8) Type "help" for help. template1=# CREATE USER intermine WITH PASSWORD 'xxxxxxx'; CREATE ROLE template1=# create database wormmine; template1=# create database items-wormmine; CREATE DATABASE template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; template1=# GRANT ALL PRIVILEGES ON DATABASE items-wormmine to intermine; template1=# \q
Tomcat
Via the package manner:
$ sudo apt-get install tomcat6
// Or via a stable binary $ curl -O http://mirror.csclub.uwaterloo.ca/apache/tomcat/tomcat-6/v6.0.33/bin/apache-tomcat-6.0.33.tar.gz $ tar -zxfv apache-tomcat-6* ; cd apache-tomcat* // startup.sh and shutdown.sh are found in apache-tomcat*/bin/
// Set up users. If installed via the package manager $ sudo emacs /etc/tomcat6/tomcat-users.xml
<tomcat-users> <role rolename="manager"/> <user username="manager" password="manager" roles="manager"/> </tomcat-users>
Edit the port in /etc/tomcat6/server.xml that Tomcat is listening on to something amenable with their architecture (for example 9999).
Data Sources
Data sources are collected at /usr/local/wormbase/intermine/data, and within that directory by version.
/usr/local/wormbase/intermine/data/WSVERSION/SOURCE/DATA_TYPE
eg:
/usr/local/wormbase/intermine/data/WS227/wormbase/gff3/ /usr/local/wormbase/intermine/data/WS227/dbsnp /usr/local/wormbase/intermine/data/WS227/uniprot
