Requirement manager for PyPPL.
It requires pyppl_annotate.
pip install pyppl_require> 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>
