snakemake-lxplus-example

Snakemake hello world example on LXPLUS and lxbatch

Setup

This is for LXPLUS 9 but it should be location independent. However, as the LXPLUS home areas have limited storage, it is recommended that you run this example under your work (e.g. /afs/cern.ch/work/f/feickert) directory.

Install pixi

Install pixi

curl -fsSL https://pixi.sh/install.sh | bash

and also enable the shell autocompletion

echo 'eval "$(pixi completion --shell bash)"' >> ~/.bashrc

and then restart shell or

. ~/.bash_profile

Run example

pixi run example

If you haven't installed the environment yet, pixi will run the equivalent of pixi install before executing your pixi run command.

Trivial lxbatch example

First run

pixi run lxbatch-init

to setup the Snakemake HTCondor profile and then run the example with

pixi run lxbatch-example