UNIX Toolkit¶

The explicit goal of this tutorial is to provide you with some tricks and tools and to make your unix life happier.

See https://github.com/stephenturner/oneliners for a bunch of examples.

Profile customization and aliases: These are ‘shortcuts’ for make doing stuff more efficient.

nano ~/.profile

alias c='clear'
alias gh='history | grep'
alias ll='logout'
alias l='ls -lth'
alias mv='mv -i'
alias cp='cp -i'


alias tn="tmux new -s"
alias ta="tmux attach -t"
alias tl="tmux ls"
alias tk="tmux kill-session -t"

DOWNLOAD SOME DATA

mkdir /home/ubuntu/data && cd /home/ubuntu/data
curl -LO https://s3.amazonaws.com/reference_assemblies/Oophaga/transcriptome/Oophaga_pumilio.1.0.0.fasta
curl -L https://github.com/ngs-docs/angus/blob/2016/_static/quantification.tgz?raw=true > quantification.tgz
tar -zxf *gz

Find a file

cd $HOME
find / -name quant.sf
find / -type f -size +10M 2> /dev/null

sed

less Oophaga_pumilio.1.0.0.fasta
sed 's/_/+++bananas+++/g' Oophaga_pumilio.1.0.0.fasta | grep ^'>' | head
sed -i 's/_/+++bananas+++/g' Oophaga_pumilio.1.0.0.fasta

A helpful guide to sed

Number fasta def line

awk '/^>/{print ">" ++i; next}{print}' < Oophaga_pumilio.1.0.0.fasta > renamed.fasta

awk

file=$(find . -name quant.sf | head -1)
awk '{print $1 "\t" $3}' $file | head
awk '$1 == "FBtr0070078"' $file

Random Stuff

cd -

TERMINATE YOUR INSTANCE¶

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