https://github.com/intermine/biotestmine
An example InterMine - for demoing and testing
https://github.com/intermine/biotestmine
Last synced: 8 months ago
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An example InterMine - for demoing and testing
- Host: GitHub
- URL: https://github.com/intermine/biotestmine
- Owner: intermine
- Created: 2018-01-29T16:12:03.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2022-08-31T09:27:06.000Z (over 3 years ago)
- Last Synced: 2025-04-02T06:51:12.789Z (10 months ago)
- Language: Shell
- Size: 26.7 MB
- Stars: 4
- Watchers: 6
- Forks: 20
- Open Issues: 3
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Metadata Files:
- Readme: README.md
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README
# README
This is an example InterMine for demo and testing.
It's used by the [tutorial](http://intermine.readthedocs.io/en/latest/get-started/tutorial), and we use it for our continuous integration tests on [Travis](https://travis-ci.org/intermine/intermine/builds)
# 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`
1. Install and start postgresql on your system
1. Create an `.intermine` directory in your $HOME directory
1. Copy [biotestmine.properties](https://github.com/intermine/biotestmine/blob/master/data/biotestmine.properties) into the `~/.intermine` directory
1. Replace PSQL_USER and PSQL_PWD with your postgres username and password.
1. (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](https://intermine.readthedocs.io/en/latest/system-requirements/software/solr/)
1. If you have tomcat running on port 8080, please stop it because it will conflict with the embedded tomcat used by the script
1. 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](https://intermine.readthedocs.io/en/latest/system-requirements/software/postgres/postgres/#character-set-encoding).