podiumASM

podiumASM [OPTIONS] COMMAND [ARGS]...

Commands

create_config: Create config.yaml for run

edit_cluster_config: Edit cluster_config.yaml use by profile

edit_tools: Edit own tools version

install_cluster: Install podiumASM on HPC cluster

install_local: Install podiumASM on local computer

run_cluster: Run workflow on HPC

run_local: Run a workflow on local computer (use singularity mandatory)

test_install: Test podiumASM with data_test after install (local or cluster)

podiumASM [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

podiumASM create_config [OPTIONS]

Options

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

edit_cluster_config

Edit cluster_config.yaml use by profile

podiumASM edit_cluster_config [OPTIONS]

edit_tools

Edit own tools version

podiumASM edit_tools [OPTIONS]

Options

-r, --restore

Restore default tools_config.yaml (from install)

Default:: False

install_cluster

Run installation of tool for HPC cluster

podiumASM 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 podiumASM commands on the bashrc file

Default:: True

install_local

Run installation for running in local computer.

The process downloading singularity images automatically.

podiumASM install_local [OPTIONS]

Options

--bash_completion, --no-bash_completion

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

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

podiumASM 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)

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 !!!

podiumASM test_install [OPTIONS]

Options

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