Website:WormMine

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Revision as of 15:25, 14 October 2011 by Tharris (talk | contribs) (→‎Postgres)
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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