culebrONT

culebrONT [OPTIONS] COMMAND [ARGS]...

Options

-r, --restore

Restore previous installation to use again “install” command

Default:: False

-e, --install_env

print Install path, Tools config, Install mode, Tools install mode, Current version, Latest version avail, Snakecdysis version

Default:: False

-v, --version: Show the version and exit.

create_config

Create configfile.yaml for run

culebrONT create_config [OPTIONS]

Options

-c, --configfile <configfile>: Required Path to create configfile.yaml

edit_profile

Edit config.yaml use by profile

culebrONT edit_profile [OPTIONS]

edit_tools

Edit own tools version

culebrONT edit_tools [OPTIONS]

Options

-r, --restore

Restore default tools_config.yaml (from install)

Default:: False

install

Run installation of tool for HPC cluster

culebrONT install [OPTIONS]

Options

-m, --mode <mode>

Mode for installation

Default:: 'slurm'
Options:: slurm | local

-e, --env <env>

Mode for tools dependencies for slurm: [‘env-modules’, ‘apptainer’], local: [‘env-modules’, ‘apptainer’]

Default:: 'apptainer'
Options:: env-modules | apptainer

--bash_completion, --no-bash_completion

Allow bash completion of culebrONT commands on the bashrc file

Default:: True

run

Run snakemake command line with mandatory parameters.
SNAKEMAKE_OTHER: You can also pass additional Snakemake parameters using snakemake syntax.
These parameters will take precedence over Snakemake ones, which were defined in the profile.
See: https://snakemake.readthedocs.io/en/stable/executing/cli.html
Example:
rattleSNP run -c configfile.yaml –dry-run –jobs 200
rattleSNP run -c configfile.yaml –threads 8 –dry-run
rattleSNP run -c configfile.yaml –apptainer-args ‘–bind /mnt:/mnt’

culebrONT run [OPTIONS] [SNAKEMAKE_OTHER]...

Options

-c, --configfile <configfile>

Required Configuration file for run tool

Default:: Sentinel.UNSET

-pdf, --pdf

Run snakemake with –dag, –rulegraph and –filegraph

Default:: False

Arguments

SNAKEMAKE_OTHER: Optional argument(s)

show_tools

show tools version

culebrONT show_tools [OPTIONS]

test_install

Test_install function downloads a scaled data test, writes a configuration file adapted to it and proposes a command line already to run !!!

culebrONT test_install [OPTIONS]

Options

-d, --data_dir <data_dir>: Required Path to download data test and create config.yaml to run test