README.md

# Environmental Cheminformatics Educational Platform: Plan B

This repository contains a collection of ansible scripts which can be
used to provision an Ubuntu/Debian based virtual machine in a public
cloud. The scripts have been written for a specific Digital Ocean
_droplet_, but can easily be adapted for something else.


## Access

The desktop environment on the compute node *alien-one* is accessible
through VNC protocol. Any VNC viewer can be used. If in doubt, try the
cross-platform TigerVNC viewer [available from here for
Windows](https://bintray.com/tigervnc/stable/download_file?file_path=vncviewer-1.11.0.exe),
or as a package from your GNU/Linux distribution. If you are neither on GNU/Linux, nor on Windows,
[here is the Java version of the viewer](https://bintray.com/tigervnc/stable/download_file?file_path=VncViewer-1.11.0.jar).



**Before** connecting, you need: 
	- A X509 certificate file (`*.pem`).
	- The IP address of the server.
	- Your username and password.

### Connection instructions

1. Open the VNC viewer.
2. Click `Options`.
3. Switch to `Security` tab.
4. Make sure that at least `TLS with X509 certificates` is checked.
5. Make sure that at least `None` is checked in the `Authentication` section.
6. Set the `Path to X509 certificate` to the location of the X509
   certificate file.
7. Now, click `OK` to accept changes and close the `Options` tab.
8. Fill in the IP address of the server in field `VNC server` and
   append `:5950` to it. So, the `VNC server` entry should look like
   this `XXX.XXX.XXX.XXX:5950`.
9. Click `Connect`.
10. **When at the login screen, ensure you are using the `Xfce Session` (settings wheel, bottom right) before entering your password**.
11. Pro-tip: User experience may be better in fullscreen (`F8` and select `fullscreen`)

## Using Environmental Cheminformatics programs

### Getting started with Shinyscreen

Shinyscreen is ECI's mass spectrum inspection program. It was written
in R and exists as a R package. In order to run it, it is necessary to
start a R session. 

While most students get to know R through R Studio, this development
environment (DE) is by no means the only one that can run R (indeed,
you do not even need a DE to run R: try it yourself, start a command
console and type `R` in there). The default choice of R DE on
`alien-one` currently is GNU Emacs with its *Emacs Speaks Statistics
(ESS)* mode.

Steps:

1. Fire up emacs
2. `Alt-x` and `R` gets you an R session
3. If asked, set your start working directory, e.g. 
`setwd('/mnt/scratch/user/')` 
(where `user` is an alias for your username)
4. Enter `library(shinyscreen)`
5. Enter `options(browser="chromium")`
6. Enter `launch()` 

To create subdirectories for different Shinyscreen calculations, 
use `dir.create()` and `setwd()` to create and set new working 
directories, respectively. This is highly recommended otherwise 
you will auto-detect and/or overwrite previous results. 


Alternatively, there there are two icons on your desktop that will
start Shinyscreen immediately without a R session. One starts the
stable version of Shinyscreen (used in this course). The other runs a
development version (you can try it out if you feel adventurous).
If you choose this path you are at the mercy of the default file path.


### Material needed for the practical

The *mzML* data files are in `/mnt/exchange` directory.

#### Just in case
1. Raw files `*.mzML` can be downloaded from [here](https://zenodo.org/record/3666069) 
2. Input files for Shinyscreen from [here](https://git-r3lab.uni.lu/eci/isb401/-/tree/master/shinyscreen_files)


### Some emacs tips
To execute a script in Emacs Ess, you have different shortcuts:

1. `Ctrl alt x`: runs a Paragraph
2. `Ctrl enter`: similar, but closer to Rstudio in how it 
treats collections of sratements
3. `Ctrl j`: runs a single line

The above commands are used when you have a separate R script that is 
being evaluated in the session. In the session itself, it's just enter