Integrate Mathjax with Gitlab

A quick (not the best way, though) way to integrate Mathjax with Gitlab. Tested on Gitlab 7.9.4 and Gitlab shell 2.6.0.

Create the file /home/git/gitlab/app/views/layouts/_mathjax.html.haml, e.g.,

sudo -u git nano /home/git/gitlab/app/views/layouts/_mathjax.html.haml

with the following content

:javascript
  (function() {
    var ga = document.createElement('script');
    ga.type = 'text/javascript';
    ga.async = true;
    ga.src = ('https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML');
    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
  })();

Then edit the file _head.html.haml

sudo -u git nano /home/git/gitlab/app/views/layouts/_head.html.haml

and change to the following (the first line already existed and the second line was newly added:

= render 'layouts/piwik' if extra_config.has_key?('piwik_url') && extra_config.has_key?('piwik_site_id')
= render 'layouts/mathjax'

Note one can control the use of mathjax just like the use of piwik.

Then restart gitlab using

sudo service gitlab restart

2015/04/07 21:29 · johnny · 0 Comments · 0 Linkbacks

Install GitLab on existing Apache2 web server

First, setup a domain to point to the server such as gitlab.example.com.

Second, follow the procedure at https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/install/installation.md till the end of Step 6. Do not proceed with 7 to install Nginx.

If you are using MySQL, remember to setup mysql database.

Third, configure apache2

Enable proxy_http
```
sudo a2enmod proxy_http
```

Create gitlab.conf with the following

<VirtualHost *:80>
        ServerName gitlab.example.com
        #git lab passthrough
        ProxyPass         / http://localhost:8080/
        ProxyPassReverse  / http://localhost:8080/
</VirtualHost>

Start apache2

sudo a2ensite gitlab.conf
sudo service apache2 reload

Configure sending emails through smtp. Add the following to /home/git/gitlab/config/environments

config.action_mailer.delivery_method = :smtp
config.action_mailer.perform_deliveries = true
config.action_mailer.raise_delivery_errors = true

config.action_mailer.smtp_settings = {
  :address              => "smtp.gmail.com",
  :port                 => 587,
  :domain               => 'gmail.com',
  :user_name            => 'account@gmail.com',
  :password             => 'password',
  :authentication       =>  :plain,
  :enable_starttls_auto => true
}

2015/04/01 15:54 · johnny · 0 Comments · 0 Linkbacks

R read data from clipboard for Windows and Mac

On Mac

On Mac Os X, the function pipe can be used to read and copy to clipboard. I often copy data from excel to clipboard and then read them into R. Specifically, the following code can be used.

dset <- read.table(pipe("pbpaste"), sep="\t")

On Windows

On Windows OS, the following can be used

x <- read.table(file = "clipboard", sep = "\t")

2014/12/16 21:28 · johnny · 0 Comments · 0 Linkbacks

R plot highlight an area under a density curve

When illustrating p-value for a given distribution, one might want to highlight / mark / shade a specific area. This can be done using the function polygon. Below is an example for an F distribution.

x<-seq(0, 10, 0.01)

y<-df(x, 2, 6)

plot(x,y,type='l', lwd=2,yaxs = "i", xaxs="i")

polygon(c(2.33,seq(2.33,10,.01),10),c(0,df(seq(2.33,10,.01),2,6),0), density = c(10, 20), angle = c(45, -45))