SnakeInstaller
- class snakecdysis.snake_wrapper.SnakeInstaller(soft_path=None, url=None, docs=None, description_tool=None, singularity_url_files=None, datatest_url_files=None, **kargs)[source]
Bases:
object
This class is used to install Snakemake workflows.
- Parameters:
soft_path (str) – The path of the wrapped workflow installation.
url (str) – URL of versioning repository (GitHub or GitLab).
docs (str) – URL of documentation.
description_tool (str) – The header printed on the terminal when running the program. Please include string values ‘VERSION’, ‘GIT_URL’, and ‘DOCS’, and the wrapper automatically replaces them with the correct values.
singularity_url_files (list(tuple())) – List of tuples 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.
snakefile (str) – Path to the main Snakemake script file (default: snakefiles/snakefile).
snakemake_scripts (str) – Path to the main Snakemake script file (default: snakefiles/snakefile).
default_profile (str) – Path to create the cluster ‘default_profile’ directory (default: default_profile/).
git_config_path (str) – Path to the default config file YAML (default: install_files/config.yaml).
git_tools_path (str) – Path to the default tools config YAML (default: install_files/tools_path.yaml).
git_cluster_config (str) – Path to the SLURM cluster config file (default: install_files/cluster_config_SLURM.yaml).
tools_version_path (str) – Path to the csv with soft and command to get version (default: report_template/versions.csv).
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 download name.
Path to the directory of cluster coockiecutter default profile.
The header print on terminal when run programme
Url of documentation
return the active path of tools config
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.
The latest workflow version, read on repository
List of tuple with downloaded url and install destination with INSTALL_PATH.
The current workflow version, read on VERSION file
Path to the main snakemake file.
Path to the scripts used on snakemake rules.
The wrapped workflow name.
Detect install mode of the tools soft, can be 'modules' or 'singularity'
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/apptainer 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
Function for know the last version of program (can be GitHub or GitLab repository)
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
tools_version_to_df
([csv_file, ...])check how tools install and get version to save on file
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
- 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.
- 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
- get_epilog() str [source]
- 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 [source]
Function for know the last version of program (can be GitHub or GitLab repository)
- get_tool_configfile()[source]
Test path of tools_path.yaml on default install path, home or argument