Git

Git is our source control software. Download and install git on your local machine.

Note InterMine is available via JCenter as executable JARs. We do not recommend downloading the InterMine source code. InterMine source code is available via GitHub.

Getting started

See Quick Start or Create Your Own InterMine for instructions on how to create a new InterMine.

Local Installation (for advanced users)

You should use the JARs available via JCenter. However, if you want to make custom changes to InterMine, you can install locally.

1. Get InterMine code.

   ~/git $ git clone https://github.com/intermine/intermine.git

2. Checkout the InterMine version you need.

   Get the list of valid tags.

   # change into the correct directory

   ~/git $ cd intermine

   # get a list of tags

   ~/git/intermine $ git tag -l

   Checkout the correct tag for the InterMine version you want to use.

   # get the correct version of the InterMine software

   ~/git/intermine $ git checkout tags/<tag_name> -b <branch_name>

3. Copy in your changes to the InterMine code.

4. Rebuild JARs locally.

Run the Maven task install to compile and create the JARs you need to run an InterMine instance.

~/git/intermine $ (cd plugin && ./gradlew clean && ./gradlew install) && (cd intermine && ./gradlew clean && ./gradlew install) && (cd bio && ./gradlew clean && ./gradlew install) && (cd bio/sources && ./gradlew clean && ./gradlew install) && (cd bio/postprocess/ && ./gradlew clean && ./gradlew install)

This places the JARs in ~/.m2/repository. You can now build a database and deploy a webapp, and your custom local JARs will be used.

Why will Maven use my JARs instead of the published JARs?

The Gradle build files are configured so that Maven looks in your local Maven (~/.m2/respository) directory first, before looking in JCenter. If Maven finds the correct version locally, those are the JARs it will use. But make sure you have the correct version!

Set your InterMine version

The InterMine version you use is determined by the system variables set in your mine's gradle.properties file.

Make sure you have your InterMine Versioning Policy set correctly. If you want to use local JARs, it's best to specify the exact version, e.g. 1.2.3, of your local JARs. Do this in your mine's gradle.properties file.

If you use 4.0.+, there's a possibility a newer version of InterMine is published. The plus sign instructs Maven to get the latest version of InterMine in any repository. In which case, Maven would use the newer JARs in JCenter instead of your local JARs.