Version 9 (modified by work@…, 11 years ago) (diff) |
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Setting up a dedicated server
In this guide we will assume you use Linux as a hosting platform. While you will be able to run GSCF on Windows, using Linux is preferable. This guide is written with Debian GNU/Linux (or Ubuntu) as a hosting platform. As Linux distributions differ other distributions may require minor changes in setup, but following this guide you should be able to get things running on other distributions as well.
Assumptions
The tutorial is based on a number of assumptions:
- you have root access to the server
- we will set up a gscf test instance on test.mysite.com on IP (1.2.3.4)
- a DNS records is available for test.mysite.com
- our database will be named 'mytestdb' with username 'mydbuser' and password 'mydbpassword'
- we will have one administrator user (user 'admin', password 'adminpw')
- we will have one default user (user 'user', password 'userpw')
Requirements
Before we can set up the server, the following requirements should be met:
- Apache Tomcat ≥ 6.x.x
- Apache Webserver ≥ 2.x (+mod_proxy, +mod_rewrite)
- PostgreSQL database server ≥ 8.4
Installation is quick and easy:
apt-get install tomcat6 postgresql-8.4 apache2 libapache2-mod-proxy-html libapache2-mod-jk
Set Up the Database
su to user postgres and create the database:
root@nmcdsp:~# su - postgres postgres@nmcdsp:~$ psql Welcome to psql 8.3.14, the PostgreSQL interactive terminal. Type: \copyright for distribution terms \h for help with SQL commands \? for help with psql commands \g or terminate with semicolon to execute query \q to quit postgres=# create database 'mytestdb'; CREATE DATABASE postgres=# create user mydbuser password 'mydbpassword'; CREATE ROLE postgres=# grant all privileges on database mytestdb to mydbuser; GRANT postgres=# grant all privileges on database mytestdb to mydbuser; GRANT postgres=# alter database mytestdb owner to mydbuser; ALTER DATABASE postgres=# \l List of databases Name | Owner | Encoding -------------+---------------+---------- mytestdb | mydbuser | UTF8 postgres | postgres | UTF8 template0 | postgres | UTF8 template1 | postgres | UTF8 (16 rows) postgres=# \q postgres@nmcdsp:~$ exit logout root@nmcdsp:~#
Set up the application configuration
Currently this is a manual step, but in the future the application will contain a getting started wizard which will do this for you (see #185).
GSCF supports externalized configuration which it expects to be in a .grails-config folder on the homedir of the tomcat user. In this case the homedir of the tomcat6 user is /usr/share/tomcat6/.grails-config so it will try to load the configuration file /usr/share/tomcat6/.grails-config/nmcdsptest-gscf.properties.
First, create the folder to hold the configuration file(s), touch an empty configuration file and change the ownership:
root@nmcdsp:~# cd /usr/share/tomcat6 root@nmcdsp:/usr/share/tomcat6# mkdir .grails-config;touch .grails-config/nmcdsptest-gscf.properties;chown -R tomcat6.tomcat6 .grails-config;chmod -R gou+rx .grails-config
Then edit the configuration file itself:
root@nmcdsp:/usr/share/tomcat6# nano .grails-config/nmcdsptest-gscf.properties
And paste the following configuration:
# Test build default configuration # # Revision Information: # $Author$ # $Date$ # $Rev$ # server URL grails.serverURL=http://test.mysite.com # DATABASE dataSource.driverClassName=org.postgresql.Driver dataSource.dialect=org.hibernate.dialect.PostgreSQLDialect dataSource.url=jdbc:postgresql://localhost:5432/mytestdb dataSource.dbCreate=update dataSource.username=mydbuser dataSource.password=mydbpassword #dataSource.logSql=false # E-MAIL # use authenticated smtp (make sure your firewall allows # outbound connections on port 465), or # - comment username and password to use non-authenticated # mail (on port 25) # - comment out all to use local mailer (e.g. postfix / # sendmail on port 25) grails.mail.host=smtp.gmail.com grails.mail.username=gscf.default.installation@gmail.com grails.mail.password=s7udycap7r3 # SpringSecurity E-Mail Settings grails.plugins.springsecurity.ui.forgotPassword.emailFrom=gscf.default.installation@gmail.com # module configuration #modules.sam.url=http://test.sam.nmcdsp.org #modules.metabolomics.url=http://test.metabolomics.nmcdsp.org #modules.metagenomics.url=http://test.metagenomics.nmcdsp.org # Number of seconds to keep rest results from modules in cache modules.cacheDuration = 600 # default application users authentication.users.admin.username=admin authentication.users.admin.password=adminpw authentication.users.admin.email=admin@mysite.com authentication.users.admin.administrator=true authentication.users.user.username=user authentication.users.user.password=userpw authentication.users.user.email=user@mysite.com authentication.users.user.administrator=false
Press CTRL-X to save the file (and enter Y).
Create a .grails directory
Grails uses a cache folder, which should be created if the tomcat user cannot create it
root@nmcdsp:~# mkdir -p /usr/share/tomcat6/.grails;chown tomcat6.tomcat6 /usr/share/tomcat6/.grails;chmod -R gou+rwx /usr/share/tomcat6/.grails
Install GSCF
Download and install the latest WAR from https://trac.nbic.nl/gscf/downloads (make sure to replace the URL and WAR names with the most recent versions).
root@nmcdsp:~# curl "https://trac.nbic.nl/gscf/downloads/8" > /tmp/gscf-0.6.6-nmcdsptest.war % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 47.8M 100 47.8M 0 0 6075k 0 0:00:08 0:00:08 --:--:-- 6602k root@nmcdsp:~# cd /var/lib/tomcat6/webapps/ root@nmcdsp:/var/lib/tomcat6/webapps# cp /tmp/gscf-0.6.6-nmcdsptest.war .;chown tomcat6.tomcat6 *.war;chmod gou+rx *.war root@nmcdsp:/var/lib/tomcat6/webapps#
Run GSCF
You should now be able to start tomcat and run the GSCF application:
root@nmcdsp:~# /etc/init.d/tomcat6 start Starting Tomcat servlet engine: tomcat6. root@nmcdsp:~#
And check if it is running properly:
root@nmcdsp:~# lynx localhost http://localhost:8080/gscf-0.6.6-nmcdsptest
Set Up Apache to proxy / rewrite request
As tomcat is running (by default) on 8080, it is not very professional to have your application run on http://test.mysite.com:8080/gscf-0.6.6-nmcdsptest. Instead http://test.mysite.com is preferable. Also it is convenient to be able to add load balancing functionality in case you expect high load. Apache can solve these issues.
First, make sure Apache loads all modules we require:
root@nmcdsp:~# cd /etc/apache2/mods-enabled/ root@nmcdsp:/etc/apache2/mods-enabled# ln -s ../mods-available/proxy* . root@nmcdsp:/etc/apache2/mods-enabled# ln -s ../mods-available/rewrite.load .
Then create a new virtual host configuration for test.mysite.com and edit it:
root@nmcdsp:/etc/apache2/mods-enabled# cd /etc/apache2/sites-available/ root@nmcdsp:/etc/apache2/sites-available# nano mysite.com_gscf-test.conf
Paste the following content into the virtual host configuration:
# Apache Virtual Host for GSCF Test Build # # Author Jeroen Wesbeek <J****n.W******@gmail.com> # Since 20100825 # # Revision Information: # $Author$ # $Date$ # $Rev$ # <VirtualHost *:80> ServerName test.mysite.com ServerAlias test.gscf.mysite.com ErrorLog /var/log/apache2/gscf-test-error.log CustomLog /var/log/apache2/gscf-test-access.log combined <IfModule mod_rewrite.c> RewriteEngine on # keep listening for the serveralias, but redirect to # servername instead to make sure only one user session # is created (tomcat will create one user session per # domain which may lead to two (or more) usersessions # depending on the number of serveraliases) # see gscf ticket #321 RewriteCond %{HTTP_HOST} ^test.gscf.mysite.com$ [NC] RewriteRule ^(.*)$ http://test.mysite.com$1 [R=301,L] # rewrite the /gscf-a.b.c-environment/ part of the url RewriteCond %{HTTP_HOST} ^test.mysite.com$ [NC] RewriteRule ^/gscf-0.6.6-nmcdsptest/(.*)$ /$1 [L,PT,NC,NE] </IfModule> <IfModule mod_proxy.c> <Proxy *> Order deny,allow Allow from all </Proxy> ProxyStatus On ProxyPass / balancer://gscf-cluster/gscf-0.6.6-nmcdsptest/ stickysession=JSESSIONID|jsessionid nofailover=On ProxyPassReverse / balancer://gscf-cluster/gscf-0.6.6-nmcdsptest/ ProxyPassReverseCookiePath /gscf-0.6.6-nmcdsptest / <Proxy balancer://gscf-cluster> BalancerMember ajp://localhost:8009 </Proxy> </IfModule> </VirtualHost>
and press CTRL-X (and Y) to save
Now enable this virtual host configuration:
root@nmcdsp:/etc/apache2# cd /etc/apache2/sites-enabled root@nmcdsp:/etc/apache2/sites-enabled# ln -s ../sites-available/mysite.com_gscf-test.conf
And reload apache to use the newly created virtual host configuration:
root@nmcdsp:/etc/apache2/sites-enabled# /etc/init.d/apache2 reload
Done
Your site should now be up and running and listening on http://test.mysite.com (and server alias test.gscf.mysite.com)