Metadata-Version: 1.2
Name: sequana_pipetools
Version: 0.6.1
Summary: A set of utilities to manager sequana pipelines
Home-page: https://github.com/sequana/sequana_pipetools
Author: thomas cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: thomas cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: 
        
        .. image:: https://badge.fury.io/py/sequana-pipetools.svg
            :target: https://pypi.python.org/pypi/sequana_pipetools
        
        .. image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg?branch=master
            :target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml
            
        .. image:: https://coveralls.io/repos/github/sequana/sequana_pipetools/badge.svg?branch=master
            :target: https://coveralls.io/github/sequana/sequana_pipetools?branch=master 
        
        .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
           :target: http://joss.theoj.org/papers/10.21105/joss.00352
           :alt: JOSS (journal of open source software) DOI
        
        :Overview: A set of tools to help building or using sequana pipelines
        :Status: Production
        :Issues: Please fill a report on `github <https://github.com/sequana/sequana/issues>`__
        :Python version: Python 3.7, 3.8
        :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352,  `JOSS DOI doi:10.21105/joss.00352 <http://www.doi2bib.org/bib/10.21105%2Fjoss.00352>`_
        
        
        What is sequana_pipetools ?
        ============================
        
        **sequana_pipetools** is a set of tools to help us managing the `Sequana <https://sequana.readthedocs.io>`_ pipelines (NGS pipelines such as RNA-seq, Variant, ChIP-seq, etc).
        
        The goal of this package is to make the deployment of `Sequana pipelines <https://sequana.readthedocs.io>`_ easier
        by moving some of the common tools used by the different pipelines in a pure
        Python library. 
        
        
        The Sequana framework used to have all bioinformatics, snakemake rules,
        pipelines, tools to manage pipelines in a single library (Sequana) as described
        in **Fig 1** here below.
        
        .. figure:: https://raw.githubusercontent.com/sequana/sequana_pipetools/master/doc/veryold.png
            :scale: 40%
        
            **Figure 1** Old Sequana framework will all pipelines and Sequana library in the same
            place including pipetools (this library).
        
        Each time we changed anything, the entire library needed to be checked carefully
        (even though we had 80% test coverage). Each time a pipeline was added, new
        dependencies woule be needed, and so on. So, we first decided to make all
        pipelines independent as shown in **Fig 2**:
        
        .. figure:: https://raw.githubusercontent.com/sequana/sequana_pipetools/master/doc/old.png
            :scale: 40%
            
            **Figure 2** v0.8 of Sequana moved the Snakemake pipelines in indepdendent
            repositories. A `cookie cutter <https://github.com/sequana/sequana_pipeline_template>`_ 
            ease the creation of scuh pipelines
        
        That way, we could change a pipeline without the need to update Sequana, and
        vice-versa. This was already a great jump ahead. Yet, some tools reprensented
        here by the *pipetools* box were required by all pipelines. This was mostly for
        providing user interface, sanity check of input data, etc. This was moving fast
        with new pipelines added every month. To make the pipelines and Sequana more
        modular, we decided to create a pure Python library that would make the
        pipelines even more independent as shown in **Fig3**. We called it
        **sequana_pipetools**.
        
        
        .. figure:: https://raw.githubusercontent.com/sequana/sequana_pipetools/master/doc/new.png
            :scale: 40%
        
            **Figure 3** New Sequana framework. The library itself with the core, the
            bioinformatics tools is now independent of the pipelines. Besides, the
            pipetools library provide common tools to all pipelines to help in their
            creation/management. For instance, common parser for options.
        
        
        
        
        Installation
        ============
        
        from pypi website::
        
            pip install sequana_pipetools
        
        No dependencies for this package except Python itself. In practice, this package
        has no interest if not used with a Sequana pipeline. So, when using it,
        you will need to install the relevant Sequana pipelines that you wish to use.
        
        This package is for `Sequana <https://sequana.readthedocs.io>`_ developers. 
        To get more help, go to the doc directory and build the local sphinx directory using::
        
            make html
            browse build/html/index.html
        
        Quick tour
        ==========
        
        There are currently two standalone tools. The first one is for Linux users under
        bash to obtain completion of a sequana pipeline command line arguments::
        
            sequana_completion --name fastqc
        
        The second is used to introspect slurm files to get a summary of the SLURM log
        files::
        
            sequana_slurm_status --directory .
        
        Will print a short summary report with common errors (if any).
        
        
        The library is intended to help Sequana developers to design their pipelines.
        See the `Sequana organization repository for examples <https://github.com/sequana>`_.
        
        In addition to those standalones, sequana_pipetools goal is to provide utilities to help Sequana developers. 
        We currently provide a set of Options classes that should be used to
        design the API of your pipelines. For example, the
        sequana_pipetools.options.SlurmOptions can be used as follows inside a standard
        Python module (the last two lines is where the magic happens)::
        
            import argparse
            from sequana_pipetools.options import *
            from sequana_pipetools.misc import Colors
            from sequana_pipetools.info import sequana_epilog, sequana_prolog
        
            col = Colors()
            NAME = "fastqc"
        
            class Options(argparse.ArgumentParser):
                def __init__(self, prog=NAME, epilog=None):
                    usage = col.purple(sequana_prolog.format(**{"name": NAME}))
                    super(Options, self).__init__(usage=usage, prog=prog, description="",
                        epilog=epilog,
                        formatter_class=argparse.ArgumentDefaultsHelpFormatter
                    )
                    # add a new group of options to the parser
                    so = SlurmOptions()
                    so.add_options(self)
        
        
        Developers should look at e.g. module sequana_pipetools.options
        for the API reference and one of the official sequana pipeline (e.g.,
        https://github.com/sequana/sequana_variant_calling) to get help from examples.
        
        
        The Options classes provided can be used and combined to design pipelines. The
        code from sequana_pipetools is used within our template to automatically create
        pipeline tree structure using a cookie cutter. This cookie cutter is available  
        in https://github.com/sequana/sequana_pipeline_template and as a
        standalone in Sequana itself (sequana_init_pipeline).
        
        What is Sequana ?
        =================
        
        **Sequana** is a versatile tool that provides 
        
        #. A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
        #. A set of Pipelines dedicated to NGS in the form of Snakefiles
           (Makefile-like with Python syntax based on snakemake framework) with more
           than 80 re-usable rules.
        #. Standalone applications.
        
        See the `sequana home page <https://sequana.readthedocs.io>`_ for details.
        
        
        To join the project, please let us know on `github <https://github.com/sequana/sequana/issues/306>`_.
        
        
        
        Changelog
        =========
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.6.1     * update schema handling
        0.6.0     * Move all modules related to pipelines rom sequana into 
                    sequana_pipetools; This release should now be the entry point for 
                    all Sequana pipelines (no need to import sequana itself).
        0.5.3     * feature removed in sequana to deal with adapter removal and
                    changes updated in the package (removed the 'design' option 
                    from the cutadapt rules and needed)
                  * Improve TrimmingOptions to provide specific list of tools 
                    and a default trimming tool
        0.5.2     * add TrimmingOptions class intended at replacing CutadaptOptions
                  * to avoid extra spaces, add '-o nospace' in all completion files
        0.5.1     * fix typo
        0.5.0     * add new module called error to be added in onerror sections of all
                    pipelines. Usual test update. Pin to stable version
        0.4.3     * add MANIFEST to include missing requirements.txt
        0.4.2     * add FeatureCounts options
        0.4.1     * add slurm status utility (sequana_slurm_status)
        0.4.0     * stable version
        0.3.1     * comment the prin_newest_version, which is too slow
        0.3.0     * stable release
        0.2.6     * previous new feature led to overhead of a few seconds with --help
                    in this version, we include it only when using --version
        0.2.5     * include newest_version feature
        0.2.4     * completion can now handle multiple directories/files properly 
                  * better doc and more tests
        0.2.3     * fix completion to avoir 2 scripts to overwrite each other
        0.2.2     * add a deprecated warning + before_pipeline function
        0.2.1     * add --from-project option to import existing config file
                  * remove --paired-data option
        0.2.0     add content from sequana.pipeline_common to handle all kind of 
                  options in the argparse of all pipelines. This is independent of 
                  sequana to speed up the --version and --help calls
        0.1.2     add version of the pipeline in the output completion file 
        0.1.1     release bug fix
        0.1.0     creation of the package
        ========= ====================================================================
        
Keywords: snakemake, sequana, RNAseq, differential analysis
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
