Session content

 Monday  - 1-7 pm Berlin time

  - Why Unix? 

  - White spaces and case sensitiveness

  - Introduction to linux commands

  - Using a Linux server - connecting and transferring files

  - Running the most popular commands

  - Manual pages: getting the most out of commands



Tuesday -   1-7 pm Berlin time

  - How do paths work? Absolute vs Relative paths

  - Increasing productivity with tab completion, shortcuts and wildcards

  - Running programs in background with Screen

  - System management - monitoring power, memory and disk space usage

  - Installing softwares and managing environments with conda



Wednesday  – 1-7 pm Berlin time

 

  - Filesystem and permission system

  - Users and groups

  - Manipulating text files with Vim

  - Turning data into information with filters

  - Searching for files in the system



Thursday -  1-7 pm Berlin time
 

  - Tabular data - definition and manipulation

  - Processing large files with AWK

  - Redirection and piping - communicating commands and files

  - Introduction to Shell scripting



Friday  -  1-7 pm Berlin time

  - Building a bioinformatics pipeline with shell 

  - Customization

Environment variables

Custom prompts

Soft links

ssh configuration

  - Final questions

  - Bonus: some other commands