![Page 1: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/1.jpg)
![Page 2: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/2.jpg)
Advanced Linux Usage
2018-02-13
Martin Dahlö[email protected]
Valentin [email protected]
Jacques [email protected]
![Page 3: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/3.jpg)
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○ 10 files? Ok○ 1000 files? Not ok (inte bra!)
![Page 7: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/7.jpg)
Multiple files
● Same program, many files○ 10 files? Ok○ 1000 files? Not ok (inte bra!)
● Reproducibility○ Self and others
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Multiple files
● Same program, many files○ 10 files? Ok○ 1000 files? Not ok (inte bra!)
● Reproducibility○ Self and others
A solution - write a script!
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Multiple files
● Same program, many files
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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
![Page 16: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/16.jpg)
Basic script
![Page 17: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/17.jpg)
Basic script
Still not OK for 1000 or more files!
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Variables
● Assigningmy_variable=5my_variable=”nice text”
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Variables
● Assigningmy_variable=5my_variable=”nice text”
● Using$my_variable
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Variables
● Assigningmy_variable=5my_variable=”nice text”
● Using$my_variable
$ my_variable=”Rackham”
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● Assigningmy_variable=5my_variable=”nice text”
● Using$my_variable
$ my_variable=”Rackham” $ echo “Hello, $my_variable! ”
Variables
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● Assigningmy_variable=5my_variable=”nice text”
● Using$my_variable
$ my_variable=”Rackham” $ echo “Hello, $my_variable! ” Hello, Rackham!
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 var in 1 2 3;do echo $vardone
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Loops
for var in text works too;do echo $vardone
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Loops
for var in mix them 5;do echo $vardone
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Loops
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Loops
Debugging!
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Loops
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Loop over files
Wildcard *
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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 condition; then
actionfi
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If
● Control statement if true; then
echo ”This is true”fi
result:This is true
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If
● Control statement if false; then
echo ”This is true”fi
result:
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If
● Control statement if [[ 5 < 9 ]]; then
echo ”This is true”fi
result:This is true
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If
● Control statement if [[ 5 > 9 ]]; then
echo ”This is true”fi
result:
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If
● Control statement if [[ 5 == 9 ]]; then
echo ”This is true”fi
result:
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If
● Control statement if [[ ”Hello” == ”Hello” ]]; then
echo ”This is true”fi
result:This is true
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If
● Control statement if [[ ”Hello” == ”Hi” ]]; then
echo ”This is true”fi
result:
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If
● Control statement if [[ ”Hello” == ”Hel”* ]]; then
echo ”This is true”fi
result: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
![Page 53: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/53.jpg)
If
● For all samples except dog
Ex: $file is /path/to/dog_1.bam
basename $file
![Page 54: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/54.jpg)
If
● For all samples except dog
Ex: $file is /path/to/dog_1.bam
basename $file
dog_1.bam
![Page 55: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/55.jpg)
If
● For all samples except dog
Ex: $file is /path/to/dog_1.bam
basename $file
dog_1.bam
![Page 56: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/56.jpg)
If
● For all samples except dog
Ex: $file is /path/to/dog_1.bam
basename $file
dog_1.bam
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Different languages
● Programming is programming○ Perl, Python, Bash, and more
![Page 58: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/58.jpg)
Different languages
● Programming is programming○ Perl, Python, Bash, and more
![Page 59: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/59.jpg)
Different languages
● Programming is programming○ Perl, Python, Bash, and more
![Page 60: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/60.jpg)
Different languages
● Programming is programming○ Perl, Python, Bash, and more
![Page 61: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/61.jpg)
Different languages
● Programming is programming○ Perl, Python, Bash, and more
● Start with one, git gud, (learn another)
![Page 62: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/62.jpg)
Different languages
● Programming is programming○ Perl, Python, Bash, and more
● Start with one, git gud, (learn another)
PYTHON
![Page 63: Advanced Linux Usage - GitHub Pages · Advanced Linux Usage 2018-02-13 Martin Dahlö martin.dahlo@scilifelab.uu.se Valentin Georgiev valentin.georgiev@icm.uu.se Jacques Dainat jacques.dainat@nbis.se](https://reader033.vdocument.in/reader033/viewer/2022052815/60a3ca171a65e9613546b1d8/html5/thumbnails/63.jpg)
Laboratory time! (yet again)