Difference between revisions of "Website:WormMine"

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Line 9: Line 9:
 
(see http://intermine.org/wiki/Prerequisites)
 
(see http://intermine.org/wiki/Prerequisites)
  
  $ sudo apt-get install postgresql
 
 
   $ sudo apt-get install sun-java6-sdk
 
   $ sudo apt-get install sun-java6-sdk
 
   $ sudo apt-get install ant
 
   $ sudo apt-get install ant
 +
 +
=== Postgres ===
 +
 +
  $ sudo apt-get install postgresql
 +
 +
Set up postgres users and create a database:
 +
 +
<pre>
 +
[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 'int3rmin3';
 +
CREATE ROLE
 +
template1=# create database wormmine;
 +
CREATE DATABASE
 +
template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine;
 +
GRANT
 +
template1=#
 +
</pre>
  
 
=== Tomcat ===
 
=== Tomcat ===
Line 34: Line 53:
  
 
Edit the port in /etc/tomcat6/server.xml that Tomcat is listening on to something amenable with their architecture (for example 9999).
 
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 ==

Revision as of 15:10, 14 October 2011

Background

Based on the Getting Started Tutorial:

   http://intermine.org/wiki/GettingStarted

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:

[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 'int3rmin3';
CREATE ROLE
template1=# create database wormmine;
CREATE DATABASE
template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine;
GRANT
template1=# 

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