Difference between revisions of "Website:WormMine"
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Data sources are collected at /usr/local/wormbase/intermine/data, and within that directory by version. | 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 | |
− | /usr/local/wormbase/intermine/data/WSVERSION/SOURCE/DATA_TYPE | ||
eg: | eg: | ||
− | /usr/local/wormbase/intermine/data/WS227/wormbase/gff3/ | + | /usr/local/wormbase/intermine/data/WS227/wormbase/gff3/ |
− | /usr/local/wormbase/intermine/data/WS227/dbsnp | + | /usr/local/wormbase/intermine/data/WS227/dbsnp |
− | /usr/local/wormbase/intermine/data/WS227/uniprot | + | /usr/local/wormbase/intermine/data/WS227/uniprot |
Revision as of 14:44, 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 postgresql $ sudo apt-get install sun-java6-sdk $ sudo apt-get install ant
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