fast5watch - Watch and archive Nanopore runs

Clojure web server application for

• watching a directory for new Nanopore runs and FAST5 files
• storing that info in a H2 DB
• archiving runs and FAST5 files to remote and/or local directories
• providing a RESTful HTTP API for accessing run and FAST5 info and files

generated using Luminus version "3.42"

Prerequisites

You will need Leiningen 2.0 or above installed.

Running

To start a web server for the application, run:

lein run 

Development

Clone repo and initialize

git clone https://github.com/peterk87/fast5watch.git
cd fast5watch

Create a dev-config.edn file for local environment variables, such as database credentials and app ports.

Example dev-config.edn

{:dev true ;; development mode
 :port 3000 ;; web server port
 ;; when :nrepl-port is set the application starts the nREPL server on load
 :nrepl-port 7000
 ;; Base Nanopore run watch directory
 :nanopore-run-base-dir "/tmp/fast5watch-test"
 ;; Database connection URL (needed for migrations)
 :database-url "jdbc:h2:./fast5watch_test.db"
 ;; H2 database name
 :dbname "./fast5watch_dev.db"
 ;; [optional] Remote archiving directory
 :remote-base-dir "/tmp/fast5watch-remote-test"
 ;; [optional] Local archiving directory
 :local-base-dir "/tmp/fast5watch-local-test"}

Initialize local H2 database:

lein run migrate

Start a web server for the app:

lein run

Connect to the nREPL.

Run lein test-refresh to run tests automatically on changes.

nREPL

Specify an :nrepl-port (e.g. 7000) in your dev-config.edn file:

{:dev true
 :port 3000
 ;; when :nrepl-port is set the application starts the nREPL server on load
 :nrepl-port 7000
 ...
 }

If using IntelliJ IDEA with the Cursive plugin, setup a remote REPL.

Run the web server for the application with:

lein run

Connect to the nREPL within IntelliJ or your editor of choice.

You should see the following in your REPL:

Connecting to remote nREPL server...
Clojure 1.10.1

Check that you can eval basic expressions:

(+ 1 1)
=> 2

Running tests

Create a test-config.edn file in the project root, e.g.:

;; test-config.edn
{:port 3000
 :database-url "jdbc:h2:./fast5watch_test.db"
 :dbname "./fast5watch_test.db"
 :nanopore-run-base-dir "/tmp/fast5watch-test-dir"}

Run tests with:

lein test
# OR recommended
lein test-refresh

It's recommended that you run lein test-refresh while developing to run tests automatically with lein-test-refresh which "is a Leiningen plug-in that automatically refreshes and then runs your clojure.test tests when a file in your project changes".

License

Copyright © Government of Canada, 2019

Written by: Peter Kruczkiewicz, National Centre for Foreign Animal Disease

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0