BlueGenes Tool Store

Development server

lein dev

Production server

lein prod

Deploying to Clojars

lein deploy

Initialising tools

The first time you start bluegenes-tool-store, all npmjs packages under the scope intermine with the keyword bluegenes-intermine-tool will be downloaded and their tool installed (for further tool management, use the BlueGenes interface).

To replicate this behaviour in a project where bluegenes-tool-store is used as a dependency, you need to add the following function call to your initialisation code.

  ;; Add the require to your ns declaration.
  (:require [bluegenes-tool-store.tools :as tools]))

    ;; In your initialisation code.
    (tools/initialise-tools)

Tool management via CLI

Note: The tools CLI doesn't give very user-friendly feedback, and is only meant as a temporary solution for older InterMine instances which don't support tool management via the BlueGenes interface due to security reasons.

If you still wish to use the tools CLI, run the following command for a usage guide.

lein tools help

If bluegenes-tool-store is used as a dependency in a different leiningen project, you can still use the tools CLI by adding "tools" ["run" "-m" "bluegenes-tool-store.tools"] to the :alises map in your project.clj.

Note on using OpenJDK 9

If you use OpenJDK 9, you will need to add the java9 profile to your leiningen task. You can do this by adding with-profile +java9 to your command, like the following:

lein with-profile +java9 <YOUR_TASK>

System requirements

• Java 8-11 (we recommend OpenJDK)
• Latest Leiningen