/nf-co.re

Code and files for the main nf-core website.

Primary LanguagePHPMIT LicenseMIT

nf-co.re

This repository contains code for the nf-core website: http://nf-co.re/

Packages used

Here's how the website is built:

Development

Getting the code

To make edits to the website, fork the repository to your own user on GitHub and then clone to your local system.

IMPORTANT: The repo has git submodules, so remember to use the --recursive flag:

git clone --recursive git@github.com:[USERNAME]/nf-co.re.git
cd nf-co.re/

If you forget the recursive flag (I always do), the markdown conversion won't work. You can pull the submodules when you realise this with the following command:

git submodule update --init --recursive

Running a local server

Ok, you're ready! To run the website locally, just start the apache-php server with:

docker-compose up

You should then be able to access the website in your browser at http://localhost:8888/.

If you prefer, you can also use a tool such as MAMP - if so, set the base directory to /path/to/nf-co.re/public_html in Preferences > Web-Server > Document Root and then hit Start Servers.

Most of the hand-written text is in /markdown, to make it easier to write. The PHP files in /public_html then parse this into HTML dynamically, if supplied with a filename.

Note that the .htaccess file is set up to remove the .php file extensions in URLs.

First-run

Much of the site is powered by a pipelines.json file. The webserver does this automatically when GitHub events trigger an update, but you'll need to run the script manually.

Access tokens

First you'll need a config.ini text file with values for github_username and github_access_token. See instructions on how to get a GitHub OAuth token (the token only needs the public_repo permission). This file is ignored in .gitignore for security reasons.

Running PHP scripts

It's easiest to run these first manual update scripts on the command line. If you have PHP available then you may be able to do this directly. Alternatively, if you are using Docker as above then you can open a shell inside the running container. The container is typically named web (you can check this with the docker ps command), so you can open an interactive shell using the following command:

docker exec -it web /bin/bash
cd var/www/

Update scripts

The following command will create public_html/pipelines.json, which is used by the website.

php update_pipeline_details.php

Note that this is also ignored in the .gitignore file and will not be tracked in git history.

Optionally, once you've done that, you can grab the pipeline traffic, issue statistics and font awesome icons:

php update_issue_stats.php
php update_stats.php
php update_fontawesome_icons.php

Note that your GitHub account needs push rights for the nf-core permission for the update_stats.php to work.

This creates nfcore_stats.json, nfcore_issue_stats.json and public_html/assets/js/fa-icons.json, all also ignored in .gitignore.

Production Server Setup

Stats cronjob

The web server needs the following cronjob running to scrape pipeline statistics once a week:

0	0	*	*	*	/usr/local/bin/php /home/nfcore/nf-co.re/update_stats.php >> /home/nfcore/update.log 2>&1
0	2	*	*	*	/usr/local/bin/php /home/nfcore/nf-co.re/update_issue_stats.php >> /home/nfcore/update.log 2>&1

The update_issue_stats.php script can use a lot of GitHub API calls, so should run at least one hour after the update_stats.php script last finished. This is not because the script takes an hour to run, but because the GitHub API rate-limiting counts the number of calls within an hour.

Tools API docs

The repo has a softlink for /tools-docs which is intended for use on the server and corresponds to the path used in public_html/deploy.php. This script pulls the built API docs from the tools repo onto the server so that it can be served at that URL.

Contribution guidelines

If you are looking forward to contribute to the website or add your institution to the official list of contributors, please have a look at the CONTRIBUTING.md.

Community

If you have any questions or issues please send us a message on Slack.

Credits

Phil Ewels (@ewels) built the website, but there have been many contributors to the content and documentation. More recently, @mashehu has done a great deal of work with the code. See the repo contributors for more.

Kudos to the excellent npm website, which provided inspiration for the design of the pipeline pages.