linux.md

Workshop - Linux re-cap

Short Linux and bash re-cap

• Linux/Bash basics + conda setup (slides)
• Another good resource: Introduction to the UNIX command line
• Cheat sheet for Bash: github.com/RehanSaeed/Bash-Cheat-Sheet
• An online linux terminal to play with

Small Cheat Sheet:

# Print your user name
echo $USER

# change directory to your user home directory (all of these are the same)
cd /home/$USER
cd $HOME
cd ~  # <- the shortest version, I like this one

# show content of current directory
ls

# make a new directory called 'myfolder'
mkdir myfolder

# generate an empty file
touch some-file.txt

# show full content of a file
cat some-file.txt

# show first 10 lines of a file
head some-file.txt

# generate three emtpy files
touch file1.txt file2.txt file3.txt

# concatenate the content of files into a new file
cat file1.txt file2.txt file3.txt > file123.txt

# ... or via a wild card
cat file?.txt > file123.txt

# compress a file 
gzip file123.txt # this will generate a compressed file 'sample.fastq.gz'

# uncompress a gz file
gunzip file123.txt.gz


# make conda/mamba environment and activate it
mamba create -n nanoplot
conda activate nanoplot
mamba install nanoplot

# Attention, the above command will create a folder 'nanoplot' in your default path, e.g. ~/miniconda3/envs
# However, you can also specify any other folder, and which we will also do in the training:
mamba create -p envs/nanoplot
conda activate envs/nanoplot
mamba install nanoplot

# run a program
NanoPlot --help

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