SnakEcdysis

class snakecdysis.snake_wrapper.SnakEcdysis(dico_tool=None, workflow=None, config=None, **kargs)[source]

Bases: SnakeInstaller

test generic wrapper class

Parameters:

soft_path (str) – The path of wrapped workflow installation
url (str) – Url of versioning repository (GitHub or GitLab)
docs (str) – Url of documentation
description_tool (str) – The header print on terminal when run programme. Please add string values ‘VERSION’, ‘GIT_URL’ and ‘DOCS’ and wrapper automatically replace by th good values
singularity_ur_files (list(tuple()) – List of tuple with downloaded url and install destination with INSTALL_PATH. like INSTALL_PATH/containers/Singularity.CulebrONT_tools.sif
datatest_url_files (tuple) – Tuple with 2 values, first the url of datatest, second download name.

Attributes Summary

`args_cluster_config`	Path to the snakemake args cluster config setting.
`args_tools_path`	Path to the user tools path setting.
`datatest_url_files`	Tuple with 2 values, first the url of datatest, second download name.
`default_profile`	Path to the directory of cluster coockiecutter default profile.
`description_tool`	The header print on terminal when run programme
`docs`	Url of documentation
`export_use_yaml`	Use to print a dump config.yaml with corrected parameters
`get_active_tools_path`	return the active path of tools config
`git_config_path`	Path to the directory of default config.yaml file.
`git_tools_path`	Path to the directory of default config.yaml file.
`git_url`	Url of versioning repository (GitHub or GitLab)
`install_mode`	Detect install mode of the soft, can be 'No install', 'local' or 'cluster'
`install_path`	The path of wrapped workflow installation.
`latest_version`	The latest workflow version, read on repository
`singularity_url_files`	List of tuple with downloaded url and install destination with INSTALL_PATH.
`snakecdysis_version`	The current workflow version, read on VERSION file
`snakefile`	Path to the main snakemake file.
`snakemake_scripts`	Path to the scripts used on snakemake rules.
`soft_name`	The wrapped workflow name.
`string_to_dag`	return command line for rule graph
`tools_mode`	Detect install mode of the tools soft, can be 'modules' or 'singularity'
`user_cluster_config`	Path to the user cluster config path setting.
`user_tools_path`	Path to the user tools path setting.
`version`	The current workflow version, read on VERSION file

Methods Summary

`check_and_download_singularity`()	Download singularity/apptainer files if provided
`check_dir_or_string`(level1, level2[, ...])	Check if the specified directory or string exists and is valid in the configuration.
`check_file_or_string`(level1, level2[, ...])	Check if path is a file if not empty :return absolute path file
`clean_home`()	Reset home's parameters of previous installation
`create_bash_completion`()	Add bash completion for version > 4.4
`fail`()	If installation fail, reset already install files
`get_config_value`(level1[, level2, level3])	get value on config_file
`get_epilog`()	Function for know the last version of program (can be GitHub or GitLab repository)
`get_last_version`()	Function for know the last version of program (can be GitHub or GitLab repository)
`get_tool_configfile`()	Test path of tools_path.yaml on default install path, home or argument
`set_config_value`(level1[, level2, value, level3])	Set config value on config_file
`tools_version_to_df`([csv_file, ...])	check how tools install and get version to save on file
`write_config`(path)	Write the corrected config file to path
`write_user_tools_path`()	Check if file is created and then write with modification of singularity path

Attributes Documentation

args_cluster_config: Path to the snakemake args cluster config setting. default to ~/.config/SOFTNAME/cluster_config_args.yaml

args_tools_path: Path to the user tools path setting. default to ~/.config/SOFTNAME/tools_path_args.yaml

datatest_url_files: Tuple with 2 values, first the url of datatest, second download name.

default_profile: Path to the directory of cluster coockiecutter default profile. install on INSTALL_PATH/default_profile

description_tool

The header print on terminal when run programme

Please add string values ‘VERSION’, ‘GIT_URL’ and ‘DOCS’ and wrapper automatically replace by the good values

docs: Url of documentation

export_use_yaml: Use to print a dump config.yaml with corrected parameters

get_active_tools_path: return the active path of tools config

git_config_path: Path to the directory of default config.yaml file. default to INSTALL_PATH/install_files/config.yaml

git_tools_path: Path to the directory of default config.yaml file. default to INSTALL_PATH/install_files/tools_path.yaml

git_url: Url of versioning repository (GitHub or GitLab)

install_mode: Detect install mode of the soft, can be ‘No install’, ‘local’ or ‘cluster’

install_path: The path of wrapped workflow installation.

latest_version: The latest workflow version, read on repository

singularity_url_files: List of tuple with downloaded url and install destination with INSTALL_PATH. like INSTALL_PATH/containers/Singularity.CulebrONT_tools.sif

snakecdysis_version: The current workflow version, read on VERSION file

snakefile: Path to the main snakemake file. Search on INSTALL_PATH/snakefiles/snakefile

snakemake_scripts: Path to the scripts used on snakemake rules. Search on INSTALL_PATH/snakemake_scripts

soft_name: The wrapped workflow name.

string_to_dag: return command line for rule graph

tools_mode: Detect install mode of the tools soft, can be ‘modules’ or ‘singularity’

user_cluster_config: Path to the user cluster config path setting. default to ~/.config/SOFTNAME/cluster_config.yaml

user_tools_path: Path to the user tools path setting. default to ~/.config/SOFTNAME/tools_path.yaml

version: The current workflow version, read on VERSION file

Methods Documentation

check_and_download_singularity(): Download singularity/apptainer files if provided

check_dir_or_string(level1, level2, mandatory=(), level3=None, check_string=False)[source]

Check if the specified directory or string exists and is valid in the configuration.

Parameters: - level1 (str): First level in the configuration hierarchy. - level2 (str): Second level in the configuration hierarchy. - mandatory (tuple): Tuple of mandatory items for the tool. - level3 (str): Optional third level in the configuration hierarchy. - check_string (bool): Flag to indicate whether to check for a string value.

Raises: - NotADirectoryError: If the specified path does not exist or is not a valid directory. - ValueError: If the path is empty when it is expected to be a string.

check_file_or_string(level1, level2, mandatory=(), level3=None, check_string=False)[source]: Check if path is a file if not empty :return absolute path file

clean_home(): Reset home’s parameters of previous installation

create_bash_completion(): Add bash completion for version > 4.4

fail(): If installation fail, reset already install files

get_config_value(level1, level2=None, level3=None)[source]: get value on config_file

get_epilog() → str

Function for know the last version of program (can be GitHub or GitLab repository): check every 30 days to skip request of if no internet connection

Return: epilogTool print at the end of header

get_last_version() → str: Function for know the last version of program (can be GitHub or GitLab repository)

get_tool_configfile(): Test path of tools_path.yaml on default install path, home or argument

set_config_value(level1, level2=None, value=None, level3=None)[source]: Set config value on config_file

tools_version_to_df(csv_file=None, active_tools_list=None, output_file=None): check how tools install and get version to save on file

write_config(path)[source]: Write the corrected config file to path

write_user_tools_path(): Check if file is created and then write with modification of singularity path