BTW this is a markdown (.md) file, it allows for quick and easy rich text formatting, that can easily be read text only and converted to other formats.

Git tutorial

conda or miniconda with Python3 is required. Installer If you want to use anything from the local conda enviroment, you have to activate the conda enviroment or add it the binaries to the system path:

source ~/miniconda3/bin/activate 

Deactivate it

source ~/miniconda3/bin/deactivate

On the linux cluster of the HS Emden/Leer we don't have acces to the .bashrc file, but it loads .bash_aliases, so a little hack after the installation completes: This overwrites the visibility of some system versions with the ones installed by the installer.

echo 'export PATH=~/miniconda3/bin:$PATH' >> ~/.bash_aliases

Make sure you have a git client installed or the git binary available. For easy acces add a ssh key to github, so that the storage of the github password is not needed.

Using conda:

conda install -c bioconda -c conda-forge snakemake

Otherwise: Global installation with pip/easyinstall

easy_install3 snakemake
#or
pip3 install snakemake