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    "info": {
        "author": "Favero Francesco",
        "author_email": "favero.francesco@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Information Technology",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: OS Independent",
            "Programming Language :: C",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: Implementation :: CPython",
            "Programming Language :: Python :: Implementation :: PyPy",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Application Frameworks",
            "Topic :: System :: Distributed Computing",
            "Topic :: Utilities"
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        "description": "BIO pype\n========\n\nSimple and slim python framework to build, organize and standardize\nbioinformatics analyses.\n\n    The system is built around the python\n    `argparse <https://docs.python.org/2/library/argparse.html>`__\n    module, to provide command line interface to run the configured\n    analyses. The framework is heavily customizable and provides basic\n    method to access to `Environment\n    Modules <http://modules.sourceforge.net>`__ and implements various\n    queuing systems such as\n    `moab/torque <http://www.adaptivecomputing.com/>`__.\n\nInstall\n-------\n\n**From Pypi**\n\n::\n\n    pip install bio_pype\n\n**The development version from git**\n\n::\n\n    git clone https://bitbucket.org/ffavero/bio_pype\n    cd bio_pype\n    python setup.py test\n    python setup.py install\n\n**Installation with virtualenv in the `computerome\nHPC <https://computerome.dtu.dk>`__ system:**\n\n(Or in any system where virtualenv is not installed at system level)\n\n::\n\n    mkdir ~/venv_files\n\n    # Download virtualenv files (not installed in the python version used in computerome)\n    curl -L -o ~/venv_files/setuptools-20.2.2-py2.py3-none-any.whl https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/setuptools-20.2.2-py2.py3-none-any.whl\n    curl -L -o ~/venv_files/pip-8.1.0-py2.py3-none-any.whl https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/pip-8.1.0-py2.py3-none-any.whl\n    curl -L -o ~/venv_files/virtualenv.py https://github.com/pypa/virtualenv/raw/develop/virtualenv.py\n\n    # Create a virtual environment\n    python ~/venv_files/virtualenv.py --extra-search-dir=~/venv_files ~/venv_bio_pype\n    # Activate the environment\n    source ~/venv_bio_pype/bin/activate\n\n    # Install bio_pype as instructed above\n\n    # The pype command line utility will be available upon the \"activation\" of the environment or by specifying the full path, in this case:\n\n    # ~/venv_bio_pype/bin/pype\n\n    # To deactivate the virtual env:\n    deactivate\n\nBasic usage\n-----------\n\nAccess first level modules:\n\n::\n\n    $ pype\n    usage: pype [-p PROFILE] {pipelines,profiles,repos,snippets} ...\n\n    Slim and simple framework to ease the managements of data, tools and pipelines in the computerome HPC\n\n    positional arguments:\n        pipelines       Workflows built by assembling pipelines and snippets\n        profiles        Set of databases softwares and meta information\n        repos           Management of pype modules\n        snippets        Single tasks implementations\n\n    optional arguments:\n      -p PROFILE, --profile PROFILE\n                        Select the profile. This will define things like\n                        databases, reference genomes paths,specific version of\n                        programs to loads and other similar configurations.\n                        Default: default\n\n    This is version 0.9.0 - Francesco Favero - 15 May 2017\n\nInstall Repos:\n--------------\n\nBy default the repository of modules is empty.\n\nTo install a desired repository, list the available repository:\n\n::\n\n    $ pype repos list -a\n\nInstall a selected repository:\n\n::\n\n    $ pype repos install -f sequenza\n\nMore Details\n------------\n\nIt is possible to pass local modules for snippets and profiles via\nenvironment variables, An example with the package test modules:\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets pype snippets\n    error: too few arguments\n    usage: pype snippets {reverse_fa,complement_fa,lower_fa,test} ...\n\n    positional arguments:\n      {reverse_fa,complement_fa,lower_fa,test}\n        reverse_fa          reverse a fasta sequence\n        complement_fa       lower case a fasta sequence\n        lower_fa            lower case a fasta sequence\n        test                test_snippets    \n\n**Snippets**\n\nThe snippets are python modules that perform a given task:\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets pype snippets test\n    error: argument --test is required\n    usage: pype snippets test --test TEST [-o OPT]\n\n    optional arguments:\n      --test TEST  Test metavar\n      -o OPT       test option\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets pype snippets test --test World\n    Hello World\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets pype snippets test --test mate -o Cheers\n    Cheers mate\n\n**Pipeline:**\n\nThe pipelines are yaml files tbat group any snippets or other pipelines,\nwith the desired dependency order.\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets PYPE_PIPELINES=test/data/pipelines pype pipelines\n    error: too few arguments\n    usage: pype pipelines [--queue {echo,none}] {rev_compl_low_fa} ...\n\n    positional arguments:\n      {rev_compl_low_fa}\n        rev_compl_low_fa   Reverse Complement Lower case a fasta\n\n    optional arguments:\n      --queue {msub,echo,none}\n                            Select the queuing system to run the pipeline\n      --log LOG             Path used to write the pipeline logs. Default working\n                            directory.\n\nThe arguments for a pipeline are parsed on the fly from a YAML file,\nwhich defines the tools and the flow of the execution:\n\n::\n\n    info:\n       description: Reverse Complement Lower case a fasta\n       date:        06/07/2016\n    items:\n      - name: lower_fa\n        type: snippet\n        arguments:\n          -i: '%(complement_fa)s'\n          -o: '%(output)s'\n        dependencies:\n          items:\n            - name: complement_fa\n              type: snippet\n              arguments:\n                -i: '%(reverse_fa)s'\n                -o: '%(complement_fa)s'\n              dependencies:\n                items:\n                  - name: reverse_fa\n                    type: snippet\n                    arguments:\n                      -i: '%(input_fa)s'\n                      -o: '%(reverse_fa)s'\n\nresulting argparse interface:\n\n::\n\n    $ PYPE_SNIPPETS=test/data/snippets PYPE_PIPELINES=test/data/pipelines pype pipelines rev_compl_low_fa\n    error: argument --complement_fa is required\n    usage: pype pipelines rev_compl_low_fa --complement_fa COMPLEMENT_FA --output\n                                           OUTPUT --reverse_fa REVERSE_FA\n                                           --input_fa INPUT_FA\n\n    optional arguments:\n      --complement_fa COMPLEMENT_FA\n                            complement_fa type: str\n      --output OUTPUT       output type: str\n      --reverse_fa REVERSE_FA\n                            reverse_fa type: str\n      --input_fa INPUT_FA   input_fa type: str\n\nMore details on `read the docs <http://bio-pype.readthedocs.io>`__\n(slowly documenting the various features/changes).\n\n\n",
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