How to run a pipeline on the CNES computing center

The CNES documentation is available here.

Setting the proxy

Follow the instructions to set a script for setting the http_proxy variables. Be careful to replace the _user variable with your proxy username: _user='http-lisa-username'.

Source this script if you need to access external resources (git clone, wget, singularity pull): source set_proxy.sh

For git clone, do not forget to use the https url.

Setting the environment

Please refer to the Running at CCIN2P3 documentation to set a virtual environement to install snakemake.

Add the following lines to your .bashrc file:

module load python/3.7.2
module load fftw
module load singularity
source venv/bin/activate
export SINGULARITY_BINDPATH="/work/SC/lisa/LDC/ancillary_data:/data"

Running the pipeline

A template script job_hal.sh is provided.

You can use screen to keep the main process alive as long as the jobs are running.