Advanced Linux Usage 2017-10-24 Martin Dahl - - PowerPoint PPT Presentation

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Sep 12, 2022 359 likes •1.02k views

Advanced Linux Usage 2017-10-24 Martin Dahl martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Shell and Bash the Shell is a Command Line Interface (CLI) Bash is one particular shell tcsh, zsh are also shell

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Advanced Linux Usage

2017-10-24 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se

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Shell and Bash

the Shell is a Command Line Interface (CLI) Bash is one particular shell tcsh, zsh are also shell programs

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Multiple files

Same program, many files

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Multiple files

Same program, many files

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Multiple files

Same program, many files

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Multiple files

Same program, many files

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Multiple files

Same program, many files

○ 10 files? Ok ○ 1000 files? Not ok..

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Multiple files

Same program, many files

○ 10 files? Ok ○ 1000 files? Not ok..

Reproducibility

○ Self and others

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Multiple files

Same program, many files

○ 10 files? Ok ○ 1000 files? Not ok..

Reproducibility

○ Self and others

The answer - write a script!

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Basic script

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Basic script

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Basic script

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Basic script

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Basic script

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Basic script

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Basic script

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Variables

Assigning

my_variable=5 my_variable=”nice text”

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Variables

Assigning

my_variable=5 my_variable=”nice text”

Using

$my_variable

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Variables

Assigning

my_variable=5 my_variable=”nice text”

Using

$my_variable $ my_variable=”Pia”

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Assigning

my_variable=5 my_variable=”nice text”

Using

$my_variable $ my_variable=”Pia” $ echo “Hello, $my_variable! ”

Variables

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Assigning

my_variable=5 my_variable=”nice text”

Using

$my_variable $ my_variable=”Pia” $ echo “Hello, $my_variable! ” Hello, Pia!

Variables

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Variables

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Variables

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Variables

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Variables

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Loops

for variable in 1 2 3; do echo $variable done

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Loops

for variable in text works too; do echo $variable done

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Loops

for variable in mix them 5; do echo $variable done

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Loops

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Loops

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Loops

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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Loop over files

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If

Control statement

if true; then

echo ”This is true”

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If

Control statement

if false; then

echo ”This is true”

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If

Control statement

if [[ 5 < 9 ]]; then

echo ”This is true”

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If

Control statement

if [[ 5 > 9 ]]; then

echo ”This is true”

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If

Control statement

if [[ 5 == 9 ]]; then

echo ”This is true”

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If

Control statement

if [[ ”Hello” == ”Hello” ]]; then

echo ”This is true”

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If

Control statement

if [[ ”Hello” == ”Hi” ]]; then

echo ”This is true”

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If

Control statement

if [[ ”Hello” == ”Hel”* ]]; then

echo ”This is true”

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If

For all samples except dog

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If

For all samples except dog

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If

For all samples except dog

Ex: $file is /path/to/dog_1.bam

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If

For all samples except dog

Ex: $file is /path/to/dog_1.bam basename $file

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If

For all samples except dog

Ex: $file is /path/to/dog_1.bam basename $file dog_1.bam

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If

For all samples except dog

Ex: $file is /path/to/dog_1.bam basename $file dog_1.bam

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If

For all samples except dog

Ex: $file is /path/to/dog_1.bam basename $file dog_1.bam

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