GNU/Linux: Introduction and Administration

4h Session for the course on "Data Science. Applications to Biology and Medicine with Python and R", at IL3 - University of Barcelona. April 2rd, 2025. 16:00h-19:00h.

https://seeds4c.org/LinuxDataScience25

Presentation Slides

SLIDES IN PDF: https://www.slideshare.net/slideshow/gnu-linux-introduction-and-administration-aed1/277441886

Video recording (from a previous edition, a few years ago)

Hands-on Exercise

Source data derived from data obtained from here:
https://analisi.transparenciacatalunya.cat/en/Medi-Ambient/Dades-meteorol-giques-de-la-XEMA/nzvn-apee

Steps:

PART A: Enter the GNU/Linux machine.
Choose one option from the following 3 options below:
1. Sign up at https://posit.cloud/plans/free to get a free account. Connect to posit.cloud and use the terminal window from the RStudio server there.
  
  OR
  .
2. Import a recent iso file form the Lubuntu GNU Linux distribution (latest Long Term Support version, 24.04 LTS as of this writing) into the VirtualBox program in your own computer.
  - ISO File:
```
https://cdimage.ubuntu.com/lubuntu/releases/noble/release/lubuntu-24.04.2-desktop-amd64.iso
```
    https://cdimage.ubuntu.com/lubuntu/releases/noble/release/lubuntu-24.04.2-desktop-amd64.iso
    .
    (Or alternatively, import an older but customized version of Lubuntu GNU Linux through, through importing the .ova file provided below for VirtualBox (explained within the session notes). OVA file: http://cloud.seeds4c.org/lubuntu_1804_64bit_v03.ova )
  .
  Keep in mind that it will take some time to download the iso (3.1 Gb) or ova file (7.6Gb), and also to import it to your Virtual Box (5-10 minutes or more),
.
PART B: Fetch and subset data
Obtain a subset of columns and rows from a dataset, using Linux simple commands in a terminal (using shell commands, not R nor Python in this case),
1. Copy the source data file (data_smc.csv.bz2 from the usb disk provided by the course professor), or from here for instance:
  http://cloud.seeds4c.org/data_smc.csv.bz2 (50Mb file, 10.000.000 rows csv file, bz2 compressed)
  
  Open a Linux terminal in your home folder /home/datascience/
```
cd /home/userNN/ # just in case, change directory to your home folder
wget http://cloud.seeds4c.org/data_smc.csv.bz2 # fetch the file from the internet
```
  xxxxxxxxxx
  
  cd /home/userNN/ # just in case, change directory to your home folder
  wget http://cloud.seeds4c.org/data_smc.csv.bz2 # fetch the file from the internet
2. Uncompress ( bunzip2 file.bz2 -k ) and show (with cat file), or use +-bzcat file.bz2 -k+- to send to standard output (stdout) on-the-fly while keeping the source compressed file (-k)
```
bunzip2 data_smc.csv.bz2 -k
```
  xxxxxxxxxx
  
  bunzip2 data_smc.csv.bz2 -k
3. filter (keep) the first 100 rows (with head -n100 file)
4. save as new file: file.csv
  
  Oneliner with the previous commands piped one after the other in the same line
```
bzcat data_smc.csv.bz2 -k | head -n100 > file_all.csv
```
  xxxxxxxxxx
  
  bzcat data_smc.csv.bz2 -k | head -n100 > file_all.csv
5. filter out one column, for instance, remove column 7 (variable _), with cut
```
cut --complement -d',' -f7 file_all.csv > file.csv
```
  xxxxxxxxxx
  
  cut --complement -d',' -f7 file_all.csv > file.csv
6. save in zip
```
zip file.csv.zip file.csv
```
  xxxxxxxxxx
  
  zip file.csv.zip file.csv
7. Change permissions so that only your user can read and write it
```
chmod 600 file.csv.zip
```
  xxxxxxxxxx
  
  chmod 600 file.csv.zip
.
PART C: Your turn
- Creativity, Exploration...
- Doubts?