Skip to main content

Requirement manager for processes of PyPPL

Project description

pyppl_require

Requirement manager for PyPPL.

Installation

It requires pyppl_annotate.

pip install pyppl_require

Usage

> pyppl require
Description:
  Process requirement manager

Usage:
  pyppl require <--pipe AUTO> [OPTIONS]

Required options:
  -p, --pipe <AUTO>     - The pipeline script.

Optional options:
  --install <AUTO>      - Install the requirements.
                          You can specify a directory (default: $HOME/bin) to install the \
                          requirements.
                          Default: None
  -h, -H, --help        - Show help message and exit.

To allow your processes to be analyzed, you have to put a section in annotate using toml format:

pXXX.config.annotate = """
@requires:
  [bedtools]
  validate: "bedtools --version"
  install: "conda install -c bioconda bedtools"
  # other annotations
"""

If you want define those commands using process properties and aggrs:

pXXX.config.annotate = """
@requires:
  [bedtools]
  validate: "{{args.bedtools}} --version"
  install: "conda install -c bioconda bedtools"
  # other annotations
"""

Install to a specify directory:

pXXX.config.annotate = """
@requires:
  [bedtools]
  validate: "{{args.bedtools}} --version"
  install: "conda install -c bioconda bedtools; ln -s $(which bedtools) {{bindir}}/bedtools"
  # other annotations
"""

{{bindir}} will be the directory passed to the command line.

pyppl require --pipe <your pipeline> --install </path/to/bin>

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pyppl-require, version 0.0.3
Filename, size File type Python version Upload date Hashes
Filename, size pyppl_require-0.0.3-py3-none-any.whl (4.4 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size pyppl_require-0.0.3.tar.gz (4.1 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page