intermine/bluegenes-tool-store

BlueGenes' Tool API server. Used as dependency in BlueGenes but can also be used standalone.

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

bluegenes-tool-store's Issues

Add support for installing a specific version of a tool, or a non-npm version

There are likely to be use cases for this at some point, but there is no burning use-case right now.

Support installing tools via Git URL

This should be supported via both the lein tools install alias and the tool store page in Bluegenes.

Using JGit would probably be enough.

Add support for tools not created by InterMine

e.g. under another namespace than @intermine, or no namespace at all. Low priority for now, perhaps pick back up if we have a genuine use case for this.

Generate tools.edn pretty-printed with indentation

This makes it easier to edit by hand.

Bundle isn't served when package.json name doesn't match folder and tools.edn name

This doesn't happen with regular use since the folder name will always be equal to the package.json name, and tools.edn will always be equal to the folder name.

However, when testing locally by using symlinks you may end up with a folder and tools.edn name that differs from the package.json name. This is also difficult to debug, since it's obvious to check that the tools.edn and folder name match, but not obvious to check the package.json name.

We should use the tools.edn name when determining the path to the bundle instead, so a differing package.json name won't have any effect.

Support installing tools via local path

This should be supported via both the lein tools install alias and the tool store page in Bluegenes.

It should create a soft/symbolic link to the tool directory and add it to tools.deps.