- Linux/Bash basics + conda setup (slides)
- Another good resource: Introduction to the UNIX command line
- small Bash 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 $HOME
cd ~ # <- the shortest version, I like this one
# show content of current directory
ls
# make a new directory called 'myfolder'
mkdir myfolder
# make conda environment and activate it
conda create -n nanoplot
conda activate nanoplot
conda install nanoplot
# run a program
NanoPlot reads.fq.gz ...- Conda is a packaging manager that will help us to install bioinformatics tools and to handle their dependencies automatically
- In the terminal enter:
# Switch to a directory with enough space
cd /scratch/$USER
# make a new folder called 'workshop'
mkdir workshop
# switch to this folder
cd workshop
# Download conda installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
# Run conda installer
bash Miniconda3-latest-Linux-x86_64.sh
# Use space to scroll down the license agreement
# then type 'yes'
# accept the default install location with ENTER
# when asked whether to initialize Miniconda3 type 'yes'
# ATTENTION: the space in your home directory might be limited (e.g. 10 GB) and per default conda installs tools into ~/.conda/envs
# Thus, take care of your disk space!
# Now start a new shell or simply reload your current shell via
bash
# You should now be able to create environments, install tools and run them- Set up conda
# add repository channels for bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge- Create and activate a new conda environment
# -n parameter to specify the name
conda create -n workshop
# activate this environment
conda activate workshop
# You should now see (workshop) at the start of each line.
# You switched from the default 'base' environment to the 'workshop' environment.Hint: An often faster and more stable alternative to conda is mamba. Funningly, mamba can be installed via conda and then used in the similar way. Just replace conda then with mamba (like shown in the bioinformatics tool slides, linked below).