Website:WormMine
From WormBaseWiki
Contents
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