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# 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. And, indeed,
they are now adapted to automate configuration of ECI workstations.


## 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. 
For Mac users, 
[here is the Java version of the viewer](https://bintray.com/tigervnc/stable/download_file?file_path=VncViewer-1.11.0.jar).
If you are on Big Sur [try this direct download](http://tigervnc.bphinz.com/nightly/osx/TigerVNC-1.11.80.dmg). 
If you are on Catalina [try this direct download](https://bintray.com/tigervnc/beta/download_file?file_path=TigerVNC-1.10.90.dmg).
If you are on El Capitan [try this direct download](https://bintray.com/tigervnc/stable/download_file?file_path=TigerVNC-1.8.0.dmg)



**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
   `XXX.XXX.XXX.XXX:5950`, or `example.somewhere.biz`.
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` (`Cmd-x` for Mac) 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~~outdated version of Shinyscreen. The other runs a
development version (~~you can try it out if you feel
adventurous~~recommended).



### 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

### Converting Shinyscreen MS2 files to MetFrag compatible format

Assuming `AAs` is the Shinyscreen project folder, to create files 
compatible with MetFrag input format follow these steps:

1. Navigate to `AAs` folder using `Thunar` file browser.
2. Right-click somewhere on the white space in the  view showing files and click on `Open Terminal Here`.
3. In the terminal, type `ls`. Is there a `MS2` folder in there? If yes, then proceed.
4. Type `ss2mf`. This command will create a `MS2_forMF` folder containing the MetFrag compatible input files.