culebrONT¶

culebrONT [OPTIONS] COMMAND [ARGS]...

Options

-r, --restore¶

Restore installation mode (need root or sudo)

Default: False

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

create_config¶

Create config.yaml for run

culebrONT create_config [OPTIONS]

Options

-c, --configyaml <configyaml>¶: Required Path to create config.yaml

edit_cluster_config¶

Edit cluster_config.yaml use by profile

culebrONT edit_cluster_config [OPTIONS]

edit_tools¶

Edit own tools version

culebrONT edit_tools [OPTIONS]

Options

-r, --restore¶

Restore default tools_config.yaml (from install)

Default: False

install_cluster¶

Run installation for HPC cluster

culebrONT install_cluster [OPTIONS]

Options

-s, --scheduler <scheduler>¶

Type the HPC scheduler (for the moment, only slurm is available ! )

Default: slurm
Options: slurm

-e, --env <env>¶

Mode for tools dependencies

Default: modules
Options: modules | singularity

--bash_completion, --no-bash_completion¶

Allow bash completion of culebrONT commands on the bashrc file

Default: True

--create_envmodule, --no-create_enmodules¶

Create a env module file allowing load culebrONT in a cluster

Default: False

-m, --modules_dir <modules_dir>¶: Directory used to save the module created by –create_envmodule parameter

install_local¶

Run installation for local computer downloading singularity images automatically.

culebrONT install_local [OPTIONS]

Options

--bash_completion, --no-bash_completion¶

Allow bash completion of culebrONT commands on the bashrc file

Default: True

run_cluster¶

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:: culebrONT run_cluster -c config.yaml –dry-run –jobs 200

culebrONT run_cluster [OPTIONS] [SNAKEMAKE_OTHER]...

Options

-c, --config <config>¶: Required Configuration file for run culebrONT

-pdf, --pdf¶

Run snakemake with –dag, –rulegraph and –filegraph

Default: False

Arguments

SNAKEMAKE_OTHER¶: Optional argument(s)

run_local¶

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:

culebrONT run_local -c config.yaml –threads 8 –dry-run

culebrONT run_local -c config.yaml –threads 8 –singularity-args ‘–bind /mnt:/mnt’

# in LOCAL using 6 threads for Canu assembly from the total 8 threads

culebrONT run_local -c config.yaml –threads 8 –set-threads run_canu=6

culebrONT run_local [OPTIONS] [SNAKEMAKE_OTHER]...

Options

-c, --config <config>¶: Required Configuration file for run culebrONT

-t, --threads <threads>¶: Required Number of threads

-p, --pdf¶: Run snakemake with –dag, –rulegraph and –filegraph

Arguments

SNAKEMAKE_OTHER¶: Optional argument(s)

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