what are the best resource to learn Linux bash scripting for Bioinformatics
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8.7 years ago
jack ▴ 960

Hi all,

I'm starting to learn bash scripting from beginning to advanced level. I'm looking for good resources or tutorial for it.

Where should I start? what are the best resources to learn it?

linux shell-script • 9.3k views
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First of all build strong foundation for your Linux administration skills. Once you get sound knowledge on that, refer different online and offline text books on Linux. If you want to build skills in Linux administration skills refer this link - http://www.kerneltraining.com/linux-admin-training/

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For those writing their first bash script, the tutorial Basic shell scripting gives you two sample DNA and protein files and takes you step by step through constructing a script for telling whether a file contains DNA or protein. You start with a very simple script that prints the contents of a file, and incrementally add steps and get them to work, until you have a final working script.

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8.7 years ago
1234Jc4321 ▴ 450

Maybe you could start by looking at those links.

http://tldp.org/LDP/abs/html/

http://wiki.bash-hackers.org/scripting/tutoriallist

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8.7 years ago
Jason ▴ 910

I like this really short tutorial on how to do some simple bash scripting. This may help getting you started or explaining a few simple concepts differently than the other post.

http://www.bashguru.com/2009/11/how-to-pass-arguments-to-shell-script.html

Here's another more extensive tutorial for beginners: http://linuxconfig.org/bash-scripting-tutorial

A quick guide: http://www.panix.com/~elflord/unix/bash-tute.html

Slightly more extensive beginners handbook on shell/bash: http://www.freeos.com/guides/lsst/

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8.6 years ago
Prakki Rama ★ 2.6k

Another one, I look frequently in unix school for my needs.

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8.6 years ago

If you're not familiar with the command line then a good place to start is:

http://ryanstutorials.net/linuxtutorial/

Then head on over to:

http://ryanstutorials.net/bash-scripting-tutorial/

for a more thorough look at scripting.

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This is a great resource for the beginners.

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8.6 years ago
Ann ★ 2.3k

I like Learning the bash shell from O'Reilly Press and use it whenever I teach Unix.

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