snakecdysis

snakecdysis [OPTIONS] COMMAND [ARGS]...

Options

-r, --restore

Restore previous installation to use again “install_local” or “install_cluster”

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 config.yaml for run

snakecdysis create_config [OPTIONS]

Options

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

edit_cluster_config

Edit cluster_config.yaml use by profile

snakecdysis edit_cluster_config [OPTIONS]

edit_tools

Edit own tools version

snakecdysis edit_tools [OPTIONS]

Options

-r, --restore

Restore default tools_config.yaml (from install)

Default:: False

install_cluster

Run installation of tool for HPC cluster

snakecdysis 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 PKGNAME commands on the bashrc file

Default:: True

install_local

Run installation for running in local computer.

The process downloading singularity images automatically.

snakecdysis install_local [OPTIONS]

Options

--bash_completion, --no-bash_completion

Allow bash completion of PKGNAME 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:
PKGNAME run_cluster -c config.yaml –dry-run –jobs 200

snakecdysis run_cluster [OPTIONS] [SNAKEMAKE_OTHER]...

Options

-c, --config <config>: Required Configuration file for run tool

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

snakecdysis run_local [OPTIONS] [SNAKEMAKE_OTHER]...

Options

-c, --config <config>: Required Configuration file for run tool

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

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

Arguments

SNAKEMAKE_OTHER: Optional argument(s)

show_tools

show tools version

snakecdysis 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 !!!

snakecdysis test_install [OPTIONS]

Options

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