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
Path to the snakemake args cluster config setting.
Path to the user tools path setting.
Tuple with 2 values, first the url of datatest, second dowmload name.
Path to the directory of cluster coockiecutter default profile.
The header print on terminal when run programme
Url of documentation
Use to print a dump config.yaml with corrected parameters
Path to the directory of default config.yaml file.
Path to the directory of default config.yaml file.
Url of versioning repository (GitHub or GitLab)
Detect install mode of the soft, can be 'No install', 'local' or 'cluster'
The path of wrapped workflow installation
List of tuple with downloaded url and install destination with INSTALL_PATH.
Path to the main snakemake file.
Path to the scripts used on snakemake rules.
The wrapped workflow name's
return command line for rule graph
Path to the user cluster config path setting.
Path to the user tools path setting.
The current workflow version, read on VERSION file
Methods Summary
Download singularity files if provided
Reset home's parameters of previous installation
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
Function for know the last version of program (can be GitHub or GitLab repository)
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
write_config
(path)Write the corrected config file to 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 dowmload 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 th good values
- docs¶
Url of documentation
- export_use_yaml¶
Use to print a dump config.yaml with corrected parameters
- 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/git_tools_path/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
- singularity_url_files¶
List of tuple with downloaded url and install destination with INSTALL_PATH. like INSTALL_PATH/containers/Singularity.CulebrONT_tools.sif
- 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’s
- string_to_dag¶
return command line for rule graph
- user_cluster_path¶
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 files if provided
- 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_last_version() str ¶
Function for know the last version of program (can be GitHub or GitLab repository)
Return: epilogTool print at the end of header