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>
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