Difference between revisions of "Website:WormMine"
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(see http://intermine.org/wiki/Prerequisites) | (see http://intermine.org/wiki/Prerequisites) | ||
− | |||
$ sudo apt-get install sun-java6-sdk | $ sudo apt-get install sun-java6-sdk | ||
$ sudo apt-get install ant | $ sudo apt-get install ant | ||
+ | |||
+ | === Postgres === | ||
+ | |||
+ | $ sudo apt-get install postgresql | ||
+ | |||
+ | Set up postgres users and create a database: | ||
+ | |||
+ | <pre> | ||
+ | [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 'int3rmin3'; | ||
+ | CREATE ROLE | ||
+ | template1=# create database wormmine; | ||
+ | CREATE DATABASE | ||
+ | template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; | ||
+ | GRANT | ||
+ | template1=# | ||
+ | </pre> | ||
=== Tomcat === | === Tomcat === | ||
Line 34: | Line 53: | ||
Edit the port in /etc/tomcat6/server.xml that Tomcat is listening on to something amenable with their architecture (for example 9999). | 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 == |
Revision as of 15:10, 14 October 2011
Background
Based on the Getting Started Tutorial:
http://intermine.org/wiki/GettingStarted
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:
[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 'int3rmin3'; CREATE ROLE template1=# create database wormmine; CREATE DATABASE template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; GRANT template1=#
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