Difference between revisions of "Administration:Installing WormMine"
From WormBaseWiki
Jump to navigationJump to search| Line 48: | Line 48: | ||
Get production branch: | Get production branch: | ||
| − | > '''git checkout remotes/origin/ | + | > '''git checkout remotes/origin/unmerged''' |
| − | <nowiki>Note: checking out 'remotes/origin/ | + | <nowiki>Note: checking out 'remotes/origin/unmerged'. |
You are in 'detached HEAD' state. You can look around, make experimental | You are in 'detached HEAD' state. You can look around, make experimental | ||
| Line 62: | Line 62: | ||
HEAD is now at 611b791... new tests, shell script to run tests | HEAD is now at 611b791... new tests, shell script to run tests | ||
</nowiki> | </nowiki> | ||
| − | > '''git checkout -b | + | > '''git checkout -b unmerged''' |
| − | Switched to a new branch ' | + | Switched to a new branch 'unmerged' |
=== Create properties file === | === Create properties file === | ||
Revision as of 18:20, 14 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
Java
Ant
Tomcat
PostgreSQL
Perl
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
