Metadata-Version: 1.1
Name: hubward
Version: 0.2.1
Summary: Manage the visualization of large amounts of other people's [often messy] genomics data
Home-page: https://github.com/daler/hubward
Author: Ryan Dale
Author-email: dalerr@niddk.nih.gov
License: BSD
Description: ``hubward``
        ===========
        
        .. image:: https://travis-ci.org/daler/hubward.svg
            :target: https://travis-ci.org/daler/hubward
        
        A common question when reading an interesting paper is, "how does relate to my
        favorite gene locus?". To address this question, usually we need to download
        the supplemental data, figure out what format it's in, convert it to some other
        useful format, and visualize it alongside our own data.
        
        `hubward` helps manage this process, lowering the effort required to track,
        manage, organize, and upload many studies for cross-comparison in the UCSC
        Genome Browser.
        
        Data are organized into `track hubs
        <https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html>`_ on the UCSC
        Genome Browser, and the name `hubward` indicates the direction in which data
        are moved into these track hubs. It can also refer to a direction in `other
        complex systems <http://wiki.lspace.org/mediawiki/Hubwards>`_.
        
        The separate repository, `hubward-studies
        <https://github.com/daler/hubward-studies>`_, contains examples of prepared
        track hubs. Subsets of these can be combined into user-defined hubs, or can
        serve as examples for preparing other studies.
        
        Documentation can be found at `<https://daler.github.io/hubward>`_.
        
        Overview
        --------
        `This poster
        <https://github.com/daler/hubward/raw/master/docs/images/hubward-poster.pdf>`_ gives an overview of `hubward`, and provides a worked example.
        
        Further details can be found in the `full documentation <https://daler.github.io/hubward>`_.
        
        
        
        
        History
        =======
        
        0.2.1 (2015-12-05)
        ------------------
        - if the `description` field is empty or missing, fill in the contents of
          README as documentation.
        - add functools32 to requirements.txt (thanks Titus Brown)
        - fixes to `hubward liftover`:
            - downloaded chainfiles are cached
            - skip tracks where assembly of track differs from the requested
              `--from_assembly`
            - upon lifting over, add a note to the description of the study's
              metadata.yaml to reflect this and also as a comment in the YAML file.
            - workaround for a bug in CrossMap on BED9+ files. The thickStart and
              thickEnd fields were not being lifted over correctly.
        - use pycurl for downloading for better handling of URL redirects. This
          happens, for example, when downloading supplemental data from ScienceDirect
        - less verbose bigbed/bigwig conversion
        - allow optional fields in metadata to be blank
        - improvements to testing framework
        
        
        0.2.0 (2015-10-24)
        ------------------
        Streamlining of the code and CLI. This causes some backward
        incompatibility with `metadata.yaml` config files in version 0.1.0, in
        particular, the "source" section is now required. There is now a defined schema
        for the metadata and the grouping files so that future changes can be validated
        and automatically fixed.
        
        
        0.1.0 (2014-01-11)
        ---------------------
        
        * First release on PyPI.
        
Keywords: hubward
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
