Clone the repo with the EFT2Obs submodule:
git clone --recursive [email protected]:TheRealLoliges486/AutoEFT2Obs.git
To create the snakemake environment (if not yet created):
mamba env create -n snakemake -f env.yaml
To source the environment do:
source env.sh
I assume that you have apptainer installed on your system. One could now run the snakemake command and it will internally pull the docker (converted by apptainer) container. However, I recommend pulling it with apptainer first
apptainer pull docker://charlotteknight/eft2obs:LO
To run the workflow first run:
snakemake --sdm apptainer --apptainer-args "--writable-tmpfs -B /afs -B /cvmfs/cms.cern.ch -B /tmp -B /etc/sysconfig/ngbauth-submit -B ${XDG_RUNTIME_DIR} -B /eos --env KRB5CCNAME='FILE:${XDG_RUNTIME_DIR}/krb5cc' " -c 1
The -c 1 tells snakemake to use one core. Specify a greater number if desired (it probably will be).
Run snakemake with --profile htcondor and without -c 1.
snakemake --sdm apptainer --apptainer-args "--writable-tmpfs -B /afs -B /cvmfs/cms.cern.ch -B /tmp -B /etc/sysconfig/ngbauth-submit -B ${XDG_RUNTIME_DIR} -B /eos --env KRB5CCNAME='FILE:${XDG_RUNTIME_DIR}/krb5cc' " --profile /afs/cern.ch/user/n/niharrin/.config/snakemake/htcondor