Administration:Installing WormMine

How to set up a development instance of WormMine

Requirements

Hardware

Linux

• 8 cores
• 24GB RAM
• ~ 1TB storage

Software

Necessary software and versions:

Software	Minimum Version	Purpose
Git	1.7	check out and update source code
Java SDK	6.0	build and use InterMine
Ant	1.8	invokes the InterMine build
Tomcat	6.0.29	website
PostgreSQL	8.3	database
Perl	5.8.8	run build scripts

Installation / configuration

Dependencies

Git

Install the command line tool:

$ sudo apt-get install git-core

Configure your user and email:

$ git config --global user.name "Name Surname"
$ git config --global user.email "your.email@gmail.com"

Java

Download here. Since InterMine can be memory intensive, it's helpful to pass environment variables to ant through the ANT_OPTS variable.

$ export ANT_OPTS="-server -XX:MaxPermSize=256M -Xmx1700m -XX:+UseParallelGC
-Xms1700m -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99"

Ant

Refer to ant's manual for installation instructions.

Tomcat

Refer to Tomcat InterMine installation

PostgreSQL

Refer to InterMine PostgreSQL installation guide

Perl

Refer to InterMine Perl installation guide

Download and Install WormMine

Navigate into the folder you want to install WormMine

Download code from Git:

~]$ git clone git@github.com:WormBase/website-intermine.git
Cloning into website-intermine...
remote: Counting objects: 2866, done.
remote: Compressing objects: 100% (1054/1054), done.
remote: Total 2866 (delta 1728), reused 2837 (delta 1699)
Receiving objects: 100% (2866/2866), 25.28 MiB | 4.65 MiB/s, done.
Resolving deltas: 100% (1728/1728), done.

This downloads the entire intermine project repository. The mine itself is a submodule of this.

Initialize submodule

~]$ cd website-intermine
website-intermine]$ git submodule update --init
Submodule 'acedb-dev/intermine' (git@github.com:WormBase/intermine.git) registered for path 'acedb-dev/intermine'
Cloning into acedb-dev/intermine...
Warning: Permanently added the RSA host key for IP address '192.30.252.131' to the list of known hosts.
remote: Counting objects: 379065, done.
remote: Compressing objects: 100% (78659/78659), done.
remote: Total 379065 (delta 233912), reused 377610 (delta 232792)
Receiving objects: 100% (379065/379065), 685.14 MiB | 6.47 MiB/s, done.
Resolving deltas: 100% (233912/233912), done. 
Submodule path 'acedb-dev/intermine': checked out 'd640534eda614d60558c6561da6fb9311d6ad893'

This populates the intermine directory at website-intermine/acedb-dev/intermine It needs to be set to the proper branch.

Navigate to the mine:

website-intermine]$ cd acedb-dev/intermine/

Get development branch:

> git checkout -b remotes/origin/unmerged
Switched to a new branch 'remotes/origin/unmerged'
> intermine]$ git pull origin unmerged
From github.com:WormBase/intermine
 * branch            unmerged   -> FETCH_HEAD 
..........

Call the directory where intermine lives, website-intermine/acedb-dev/intermine, <INTERMINE DIR>

Create properties file

• Create ~/.intermine directory.
• Copy the sample properties file as ~/.intermine/wormmine.properties
• Fill in placeholders as follows:
  • <POSTGRES USER PASSWORD>: postgres password for intermine user
  • <TOMCAT USER PASSWORD>: tomcat password for intermine user
  • <SERVER PUBLIC BASE URL>: Base url of your web server, including port. Sample: http://123.456.789.123:8080
  • <CREATE WM ADMIN USERNAME/PASSWORD> create the primary admin account
  • <EMAIL ADDRESS TO SEND HELP EMAILS FROM>: your server should be configured to send emails from this address. This will send users password reset emails and the like.
  • <HELP REQUESTS ARE SENT HERE>: can be same address as above, this is where input from the InterMine help form gets sent.

Get production database

Instantiate database dump

To instantiate a previously built WormMine production database.

• Find your favorite release from WORMMINE DB FTP URL (placeholder, no URL exists)
• Create empty DB

> createdb -U intermine -E SQL_ASCII wormmine

• • -U: user set to intermine
  • -E: character set used
• Unpack and restore DB

> psql -U intermine -d wormmine -f <WORMMINE RELEASE SQL>

• • -U: execute as user
  • -d: destination DB
  • -f: SQL input file

Create userprofile database

InterMine needs a separate database to track users and their information.

• Create empty DB

> createdb -U intermine -E SQL_ASCII userprofile-wormmine

• Build the userprofile DB

> cd <INTERMINE DIR>/webapp
> ant build-db-userprofile

Launch webapp

• Navigate to intermine/wormmine/webapp
• Launch webapp:

 > ./xx

• • This script contains:

ant clean
ant -v default remove-webapp release-webapp

Test Webapp

You should be able to reach your new instance through <baseurl>/wormmine Webapp is standalone.

Attach to WormBase instance

If you want to enable integration with WormBase, follow these steps:

Checkout merged branch

> git checkout remotes/origin/staging
Note: checking out 'remotes/origin/staging'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 611b791... new tests, shell script to run tests

> git checkout -b staging
Switched to a new branch 'staging'

Reconfigure properties file

• Needs to deploy at tools/wormmine

webapp.path=tools/wormmine

• Change url to where the base will be:

webapp.baseurl=http://staging.wormbase.org
webapp.returnurl=http://staging.wormbase.org/auth/openid?openid_identifier=https://www.google.com/accounts/o8/id&redirect=http://dev.wormbase.org/tools/wormmine/mymine.do#

Modify wormbase.conf

To enable login system, make sure config flag: wormmine_path = 'tools/wormmine' is uncommented.