README.md

README

This is an example InterMine for demo and testing.

It's used by the tutorial, and we use it for our continuous integration tests on Travis

Building the mine

Mac OSX note

1. Install wget if it's not already installed.
   1. Install homebrew if not already installed: https://brew.sh/
   2. brew install wget

Linux and OSX

This mine can be built with the ./setup.sh script. Steps:

1. Install Perl module dependencies: sudo cpan XML::Parser::PerlSAX Text::Glob Cwd Getopt::Std
2. Install and start postgresql on your system
3. Create an .intermine directory in your $HOME directory
4. Copy biotestmine.properties into the ~/.intermine directory
5. Replace PSQL_USER and PSQL_PWD with your postgres username and password.
6. (Optional) Initialise the two search repositories used by InterMine. If you don't do this, the keyword search won't work in your mine. Follow the instructions for Solr
7. If you have tomcat running on port 8080, please stop it because it will conflict with the embedded tomcat used by the script
8. Run build script in your biotestmine repository: ./setup.sh Note: If you get an error related to SQL_ASCII, you could either use DB_ENCODING=UTF-8 ./setup.sh or follow the documentation to set postgresql to use SQL_ASCII.