Difference between revisions of "Administration:Installing WormMine"
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== Dependencies == | == Dependencies == | ||
=== Git === | === Git === | ||
| + | Install the command line tool: | ||
| + | |||
| + | <code>$ sudo apt-get install git-core</code> | ||
| + | |||
| + | Configure your user and email: | ||
| + | <code>$ git config --global user.name "Name Surname" | ||
| + | $ git config --global user.email "your.email@gmail.com" | ||
| + | </code> | ||
| + | |||
=== Java === | === Java === | ||
| + | Download [http://java.com/en/download/index.jsp here]. | ||
| + | Since InterMine can be memory intensive, it's helpful to pass environment variables to ant through the <code>ANT_OPTS</code> variable. | ||
| + | |||
| + | <code>$ export ANT_OPTS="-server -XX:MaxPermSize=256M -Xmx1700m -XX:+UseParallelGC | ||
| + | -Xms1700m -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99" | ||
| + | </code> | ||
| + | |||
=== Ant === | === Ant === | ||
| + | Refer to [http://ant.apache.org/manual/index.html ant's manual] for installation instructions. | ||
| + | |||
=== Tomcat === | === Tomcat === | ||
| + | Refer to [http://intermine.readthedocs.org/en/latest/system-requirements/software/tomcat/ Tomcat InterMine installation] | ||
| + | |||
=== PostgreSQL === | === PostgreSQL === | ||
| + | Refer to [http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/ InterMine PostgreSQL installation guide] | ||
| + | |||
=== Perl === | === Perl === | ||
| + | Refer to [http://intermine.readthedocs.org/en/latest/system-requirements/software/perl/ InterMine Perl installation guide] | ||
| + | |||
== Download and Install WormMine == | == Download and Install WormMine == | ||
Revision as of 14:53, 16 August 2013
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/intermine.git Cloning into intermine... remote: Counting objects: 378842, done. remote: Compressing objects: 100% (78542/78542), done. remote: Total 378842 (delta 233731), reused 377487 (delta 232710) Receiving objects: 100% (378842/378842), 684.97 MiB | 9.16 MiB/s, done. Resolving deltas: 100% (233731/233731), done.
Get production branch:
> git checkout remotes/origin/unmerged Note: checking out 'remotes/origin/unmerged'. 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 unmerged Switched to a new branch 'unmerged'
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
- Find your favorite release from WORMMINE DB FTP URL
- 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
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.
