auto_process_ngs.conda
Module providing utility classes and functions to help with managing
conda
environments:
CondaWrapper: wrapper for
conda
, including environment creationCondaWrapperException: base class for exceptions from CondaWrapper
CondaCreateEnvError: exception for errors when creating environments
make_conda_env_name: construct consistent names for conda environments
- exception auto_process_ngs.conda.CondaCreateEnvError(message=None, env_name=None, status=None, cmdline=None, output=None)
Exception raised when CondaWrapper class fails to create a new environment
- Parameters:
message (str) – error message
env_name (str) – name of the environment
status (int) – status returned by the conda command
cmdline (str) – command line for the conda command that generated the error
output (str) – output from the conda command
- class auto_process_ngs.conda.CondaWrapper(conda=None, env_dir=None, channels=None)
Class for installing conda and creating environments
Example usage:
>>> conda = Conda('/usr/local/miniconda/bin/conda', ... channels=('bioconda','conda-forge'), ... env_dir='_conda_envs') >>> conda.install() >>> conda.create_env('multiqc@1.9','multiqc=1.9')
- activate_env_cmd(name)
Fetch command to activate a conda environment
- Parameters:
name (str) – name/path of the environment to activate
- Returns:
- Command instance to activate the
named environment.
- Return type:
- property conda
Path to conda executable
- create_env(name, *packages, **args)
Create a new conda environment
- Parameters:
name (str) – name of the new environment
packages (list) – package specifications for packages to install (e.g. ‘fastqc=0.11.3’)
- property env_dir
Path to the directory for conda environments
- install()
Install conda
Downloads and runs the miniconda installer if conda is not already installed
- property is_installed
Check whether conda is installed
- property list_envs
Return a list of environments in the ‘envs’ directory
- verify_env(name)
Check whether conda environment can be activated
- Parameters:
name (str) – name/path of the environment to check
- Returns:
- True if activate command returned status
zero, False otherwise.
- Return type:
Boolean
- property version
Return the conda version
- exception auto_process_ngs.conda.CondaWrapperError
Base class for conda-specific exceptions
- auto_process_ngs.conda.make_conda_env_name(*pkgs)
Return a name for a conda env based on package list
Constructs a name for a conda environment, based on the packages specified for inclusion in the environment.
The name consists of components of the form “NAME[@VERSION]” for each package specification “NAME[=VERSION]” (e.g. ‘star=2.4.2a’ becomes ‘star@2.4.2a’).
Components are joined by ‘+’ and are sorted by package name (regardless of the order they are supplied in).
- Parameters:
pkgs (list) – list of conda package specifiers
- Returns:
- environment name constructed from package
list.
- Return type:
String