Website:WormMine

Background

Based on the Getting Started Tutorial:

   http://intermine.org/wiki/GettingStarted

Getting the source

You'll need both the intermine source code as well as the wormbase "website-intermine" repository. These should be stored side-by-side to maintain paths.

> cd ~/projects   // or whatever
> mkdir intermine ; cd intermine
> svn co svn://subversion.flymine.org/branches/intermine_0_98
> ln -s intermine_0_98 intermine
> git clone git@github.com:WormBase/website-intermine.git
> ls ~/projects/intermine
total 8
lrwxrwxrwx  1 tharris tharris    14 2011-10-14 14:13 intermine -> intermine_0_98 
drwxrwxr-x 13 tharris tharris  4096 2011-10-14 14:13 intermine_0_98
drwxr-xr-x  5 tharris wormbase 4096 2011-10-14 14:27 website-intermine  

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