OpenTreeOfLife/files.opentreeoflife.org

Name: files.opentreeoflife.org

Owner: OpenTreeOfLife

Description: Static content related to the project; the webroot for the files.opentreeoflife.org web site. The repo contains all of the smallish files: indexes, READMEs, and so on. Larger files such as taxonomies and synthetic trees on the web site but not in git.

Created: 2015-06-26 15:08:45.0

Updated: 2016-01-21 20:55:39.0

Pushed: 2017-03-09 20:55:10.0

Homepage: null

Size: 425

Language: HTML

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README

How to make changes to the files.opentreeoflife.org site

(See the germinator repository's wiki for Open Tree of Life documentation.)

The site is served from the directory ~opentree/files.opentreeoflife.org/ on host files.opentreeoflife.org. The web root is a git checkout of the files.opentreeoflife.org github repository.

There are two kinds of files in this tree: “large” and “small”.

1. The small files - mostly index.html files - are maintained in the files.opentreeoflife.org github repository.
2. The large files (e.g. versions of OTT or the synthetic tree) are simply copied from wherever they originate to the appropriate place in this tree. They are backed up elsewhere (currently varela.csail.mit.edu).

It is useful to have a 'files' alias in you .ssh/config.

The small files can be updated in any of three ways:

Push method

Clone the files.opentreeoflife.org repository locally, or bring it up to date if you've already cloned it ('git pull'). Update the small files you want to change in your local clone and commit to github. Then refresh the web site from github by logging in and doing 'git pull' in the ~opentree/files.opentreeoflife.org directory.

echo "cd files.opentreeoflife.org && git pull && make" | ssh files

The 'make' is only necessary if you change a markdown file that has to be converted to HTML.

Using branches and the PR process seems a bit heavyweight for this site. I'm OK with committing directly to master for now. We can switch to a more rigorous process if that leads to trouble.

Pull method

Edit the files in place on the server. Then copy them using scp back to your local checkout of the files.opentreeoflife.org repo. Branch, commit, push, PR.

Checking your markdown

Remember that if you want to write web pages for the site in markdown format, they have to be converted to HTML for them to work on the web. This is what the top level Makefile is for.

Here is how I check markdown locally before committing it to github:

perl ~/Downloads/Markdown_1.0.1/Markdown.pl README.md  >foo.html && open foo.html

The download link is here.