https://github.com/pwwang/pyppl_require

Process requirement manager for PyPPL
https://github.com/pwwang/pyppl_require

Last synced: 14 days ago
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Process requirement manager for PyPPL

• Host: GitHub
• URL: https://github.com/pwwang/pyppl_require
• Owner: pwwang
• License: mit
• Created: 2019-12-12T19:50:11.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2020-06-06T04:42:06.000Z (over 4 years ago)
• Last Synced: 2024-12-10T04:27:01.855Z (24 days ago)
• Language: Python
• Size: 43 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# pyppl_require

Requirement manager for [PyPPL](https://github.com/pwwang/PyPPL).

## Installation

It requires [pyppl_annotate](https://github.com/pwwang/pyppl_annotate).

```shell

pip install pyppl_require

```

## Usage

```shell

> pyppl require

Description:

  Process requirement manager

Usage:

  pyppl require <--pipe AUTO> [OPTIONS]

Required options:

  -p, --pipe      - The pipeline script.

Optional options:

  --install       - 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:

```python

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:

```python

pXXX.config.annotate = """

@requires:

  [bedtools]

  validate: "{{args.bedtools}} --version"

  install: "conda install -c bioconda bedtools"

  # other annotations

"""

```

Install to a specify directory:

```python

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.

```shell

pyppl require --pipe  --install 

```