Difference between revisions of "Website:WormMine"
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== Users and Groups == | == Users and Groups == | ||
+ | sudo groupadd wormbase | ||
sudo adduser -M intermine // will be the user connecting to the mine database | sudo adduser -M intermine // will be the user connecting to the mine database | ||
sudo passwd intermine xxxxxx | sudo passwd intermine xxxxxx | ||
+ | sudo useradd tharris // not strictly required of course | ||
+ | sudo usermod -a -G wormbase,intermine tharris | ||
== Getting the source == | == Getting the source == |
Revision as of 17:22, 13 January 2012
Contents
Background
Based on the Getting Started Tutorial:
http://intermine.org/wiki/GettingStarted
Users and Groups
sudo groupadd wormbase sudo adduser -M intermine // will be the user connecting to the mine database sudo passwd intermine xxxxxx sudo useradd tharris // not strictly required of course sudo usermod -a -G wormbase,intermine tharris
Getting the source
You'll need both the intermine source code as well as various wormbase "website-intermine" repositories.
> cd /usr/local/wormbase // or whatever > mkdir intermine ; cd intermine > svn co svn://subversion.flymine.org/branches/intermine_0_98 > ln -s intermine_0_98 intermine
Fetch the WormBase-specific elements of intermine, currently maintained as separate repositories.
// The master directory, containing model and code for fetching/parsing datasets > cd intermine > git clone http://github.com/WormBase/website-intermine-master wormmine // sources > cd bio/sources > git clone git://github.com/WormBase/website-intermine-sources.git wormmine
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:
TH: THIS IS A HACK. I don't fully grok postgres' authentication config.
[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 'xxxxxxx'; CREATE ROLE template1=# create database wormmine; template1=# create database items-wormmine; CREATE DATABASE template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine; template1=# GRANT ALL PRIVILEGES ON DATABASE items-wormmine to intermine; template1=# \q
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
WormBase specific modifications
The following directories currently contain WormMine-specific modifications that are NOT under version control:
- The entire intermine/wormmine directory. Relocating it and symlinking intermine/wormine -> our/source/repo doesn't work.
- The intermine/bio/sources directory. This *can* be relocated in wormmine/project.xml, but build paths in sources need to be updated, too.