Introduction to Programming - Linux (2018 - 2019)

In the first lecture, we will have a short introduction to Linux and we will see some advantages of using Linux instead of other Operating Systems.

Outline
---------

• Some historical, technical and general facts about Linux
• The Linux directory structure
• Linux command line
• ls, cd, mkdir, rm, cp, mv
• history, man
• creating files

Outline
---------

• Basic editors: nano, pico etc
• Linux command line
• more, less, head, tail
• apt-get
• redirection: pipes, writing to files

(lecture notes: see class 2)

Outline
---------

• Linux command line
• grep, cut, less, xargs
• pipes
• Emacs editor
• Create scripts
• The PATH Variable

Tasks
--------

• Study the first 35 pages (up to 1.7) of the document (BOOK) and try to understand the examples.
• Also, check the first pages of this BOOK2 (up to Specialized Navigation and History).

Exercises
----------------
DEADLINE 7 November 2018

http://rpubs.com/idaios/Exercises_Lec4

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 Linux_commands

Exercises are here

http://rpubs.com/idaios/linux20181113

deadline 26/11/2018

Basic AWK functionality and commands

Lecture notes: AWK_basics.pdf

Exercises: AWK_exercises.pdf

File for exercises: AWK_directory.txt

BLAST basics

Downloading & configuring BLAST, getting info about BLASTDBs, running BLAST, creating BLAST DBs

Lecture notes: BLAST_tutorial_2018.pdf

BLAST algorithm basic information: BLAST_basic.pdf

Tabular Data File Processing  via GAWΚ (and other unix command line tools)
Read
Select
Merge (join)
Compute

Introduction to HPC

Tutorial for accessing, submitting and monitoring tasks at IMBBC HPC

Job submission and monitoring

mafft example