Metadata-Version: 2.1
Name: janis pipelines
Version: 0.2.7
Summary: Contains classes and helpers to build a workflow, and provide options to convert to CWL / WDL
Home-page: https://github.com/PMCC-BioinformaticsCore/janis
Author: Michael Franklin, Evan Thomas, Mohammad Bhuyan
Author-email: michael.franklin@petermac.org
License: GNU
Description: # Janis
        _Portable pipelines assistant_
        
        [![Build Status](https://travis-ci.org/PMCC-BioinformaticsCore/janis.svg?branch=master)](https://travis-ci.org/PMCC-BioinformaticsCore/janis)
        [![Documentation Status](https://readthedocs.org/projects/janis/badge/?version=latest)](https://janis.readthedocs.io/en/latest/?badge=latest)
        [![PyPI version](https://badge.fury.io/py/janis-pipelines.svg)](https://badge.fury.io/py/janis-pipelines)
        
        ## Quickstart
        
        Install through PIP ([project page](https://pypi.org/project/janis-pipelines/)):
        ```
        pip install janis-pipelines
        ```
        
        And ReadTheDocs: https://janis.readthedocs.io/en/latest/
        ___
        OR
        
        Clone the [GitHub repository](https://github.com/PMCC-BioinformaticsCore/janis):
        ```bash
        git clone git@github.com:PMCC-BioinformaticsCore/janis.git
        ```
        
        
        ## About
        
        This project was produced as part of the Portable Pipelines Project in partnership with:
        - [Melbourne Bioinformatics (University of Melbourne) ](https://www.melbournebioinformatics.org.au/)
        - [Peter MacCallum Cancer Centre](https://www.petermac.org/)
        - [Walter and Eliza Hall Institute of Medical Research (WEHI) ](https://www.wehi.edu.au/)
        
        ### Related project links:
        - Janis:
            - Janis Documentation: https://janis.readthedocs.io/en/latest/
            - Janis Git: https://github.com/PMCC-BioinformaticsCore/janis
            - Janis PyPi: https://pypi.org/project/janis-pipelines/
            - Janis Bioinformatics: 
                - Git: https://github.com/PMCC-BioinformaticsCore/janis-bioinformatics
                - PyPi: _Coming soon_
        
        - CWLGen (forked): https://github.com/illusional/python-cwlgen
        - WDLGen: https://github.com/illusional/python-wdlgen
        
        
        ## Usage
        
        You must import `janis` into your project, that is:
        ```python
        import janis as j
        ``` 
        
        ### Included definitions
        
        Some unix tools have been wrapped and included as part of the pip module. They are located at `janis.unix.tools/`.
        The examples will use the included unix tools, with more information about bioinformatics tools down below. 
        See the section about contributions if you find an error in the tool definitions.
        
        ### Creating workflows
        
        A Workflow consists of inputs, outputs and steps (which each have their own tool).
        You can connect these components together with edges. Let's look the simple untar workflow.
        
        ```python
        import janis as j
        from janis.unix.tools.echo import Echo 
        
        w = j.Workflow("workflow_identifier")
        
        inp = j.Input("input_identifier", p.String())
        step = j.Step("step_identifier", Echo())
        outp = j.Output("output_identifier")
        
        w.add_pipe(inp, step, outp)
        
        # Will print the CWL, input file and relevant tools to the console
        w.dump_translation("cwl", to_disk=False)
        ```
        
        
        ## Bioinformatics tools and data types
        
        _Coming soon_
        
        A repository of bioinformatic tools will be build to use within this pipeline. 
        The git submodule is embedded here for reference, but can also be found here: [here](https://github.com/PMCC-BioinformaticsCore/pipelines-bioinformatics).
        
        ### Intended usage
        
        ```
        pip install janis-pipelines[bioinformatics]
        ```
        
        Then you can simple import:
        ```
        import janis.bioinformatics
        ```
        
        
        ## Contributions
        
        Contributions are the bread and butter of open source, and we welcome contributions. 
        All sections of this module are written in Python, however a fair understanding of Workflows, CWL or WDL 
        might be required to make changes.
        
        If you find an issue with Pipeline related functionality, please report it through the 
        [Github issues page](https://github.com/PMCC-BioinformaticsCore/janis/issues).
        
        If you find an issue with the tool definitions, please see the relevant issue page:
        - [Pipeline-bioinformatics](https://github.com/PMCC-BioinformaticsCore/pipelines-bioinformatics/issues)
        
        
        
        ### Releasing Portable Pipelines
        
        Releasing is automatic! Simply increment the version number in `setup.py` ([SemVer](https://semver.org)), 
        and tag that commit with the same version identifier:
        ```
        git tag -a "v0.x.x" -m "Tag message"
        git push --follow-tags
        ```
        
        [Travis](https://travis-ci.org/PMCC-BioinformaticsCore/janis) will automatically build the repository, 
        run the associated unit tests and if they succeed, deploy to [PyPi](https://pypi.org/project/janis-pipelines/). 
        
        
        And that's it!
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Provides-Extra: bioinformatics
