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¶
culebrONT install_local [OPTIONS]
Options
- --bash_completion, --no-bash_completion¶
Allow bash completion of culebrONT commands on the bashrc file
- Default
True
run_cluster¶
- 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¶
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