{ "info": { "author": "Ryan Dale", "author_email": "dalerr@niddk.nih.gov", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: BSD License", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "``hubward``\n===========\n\n\n.. image:: https://travis-ci.org/daler/hubward.svg\n :target: https://travis-ci.org/daler/hubward\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square\n :target: http://bioconda.github.io\n\nA common question when reading an interesting paper is, \"how does relate to my\nfavorite gene locus?\". To address this question, usually we need to download\nthe supplemental data, figure out what format it's in, convert it to some other\nuseful format, and visualize it alongside our own data.\n\n`hubward` helps manage this process, lowering the effort required to track,\nmanage, organize, and upload many studies for cross-comparison in the UCSC\nGenome Browser.\n\nData are organized into `track hubs\n`_ on the UCSC\nGenome Browser, and the name `hubward` indicates the direction in which data\nare moved into these track hubs. It can also refer to a direction in `other\ncomplex systems `_.\n\nThe separate repository, `hubward-studies\n`_, contains examples of prepared\ntrack hubs. Subsets of these can be combined into user-defined hubs, or can\nserve as examples for preparing other studies.\n\nDocumentation can be found at ``_.\n\nOverview\n--------\n`This poster\n`_ gives an overview of `hubward`, and provides a worked example.\n\nFurther details can be found in the `full documentation `_.\n\n\n\n\nHistory\n=======\n\n0.2.2 (2016-01-20)\n------------------\n- Support for liftover of BAMs (includes a workaround for Crossmap bug that\n segfaulted on liftovers with a specified output filename in the test\n environment).\n- When lifting over between assemblies and the source assembly doesn't match\n what is configured for a track, raise a ValueError.\n- For lifted-over studies, the `metadata.yaml` config keeps track of the\n liftover history in the new `study/liftover` section\n- improved test environment setup\n- improved tests (checking for existence of uploaded files)\n\n\n0.2.1 (2015-12-05)\n------------------\n- if the `description` field is empty or missing, fill in the contents of\n README as documentation.\n- add functools32 to requirements.txt (thanks Titus Brown)\n- fixes to `hubward liftover`:\n - downloaded chainfiles are cached\n - skip tracks where assembly of track differs from the requested\n `--from_assembly`\n - upon lifting over, add a note to the description of the study's\n metadata.yaml to reflect this and also as a comment in the YAML file.\n - workaround for a bug in CrossMap on BED9+ files. The thickStart and\n thickEnd fields were not being lifted over correctly.\n- use pycurl for downloading for better handling of URL redirects. This\n happens, for example, when downloading supplemental data from ScienceDirect\n- less verbose bigbed/bigwig conversion\n- allow optional fields in metadata to be blank\n- improvements to testing framework\n\n\n0.2.0 (2015-10-24)\n------------------\nStreamlining of the code and CLI. This causes some backward\nincompatibility with `metadata.yaml` config files in version 0.1.0, in\nparticular, the \"source\" section is now required. There is now a defined schema\nfor the metadata and the grouping files so that future changes can be validated\nand automatically fixed.\n\n\n0.1.0 (2014-01-11)\n---------------------\n\n* First release on PyPI.", "description_content_type": null, "docs_url": "https://pythonhosted.org/hubward/", "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/daler/hubward", "keywords": "hubward", "license": "BSD", "maintainer": null, "maintainer_email": null, "name": "hubward", "package_url": "https://pypi.org/project/hubward/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/hubward/", "project_urls": { "Download": "UNKNOWN", "Homepage": "https://github.com/daler/hubward" }, "release_url": "https://pypi.org/project/hubward/0.2.2/", "requires_dist": null, "requires_python": null, "summary": "Manage the visualization of large amounts of other people's [often messy] genomics data", "version": "0.2.2" }, "last_serial": 1914203, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "1c97f2c3aa1765b6646f72d0386f0bfc", "sha256": "4a3367ef4a376a066163793f320571d34bbab2f3faf4bd708771b0c50e3b8a4b" }, "downloads": -1, "filename": "hubward-0.1.0.tar.gz", "has_sig": false, "md5_digest": "1c97f2c3aa1765b6646f72d0386f0bfc", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 25848, "upload_time": "2015-08-18T19:48:47", "url": "https://files.pythonhosted.org/packages/4e/bc/212470bd0f2228d50a6d5ae180896aa43a1e24da9c93cbe194256299a448/hubward-0.1.0.tar.gz" } ], "0.2.0": [ { "comment_text": "", "digests": { "md5": "566915f4acc6af07eb32a50fd3a3a1fc", "sha256": "ff8b55d54b392e8e8ef2be6b4090fe42e5288a0150145727c8555f1ff5f406a4" }, "downloads": -1, "filename": "hubward-0.2.0.tar.gz", "has_sig": false, "md5_digest": "566915f4acc6af07eb32a50fd3a3a1fc", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 42776, "upload_time": "2015-10-28T18:50:49", "url": "https://files.pythonhosted.org/packages/66/6e/f6a23ef87bdd3e6dd048b5b41700ecf55dd9cf75d792ce1a5418711a6da7/hubward-0.2.0.tar.gz" } ], "0.2.1": [ { "comment_text": "", "digests": { "md5": "c67418580f119d159212b8acfe66bf00", "sha256": "7148973b240453b0c2e40c2a69267362501fa70c64bbce0f9a4bd288db38aeb9" }, "downloads": -1, "filename": "hubward-0.2.1.tar.gz", "has_sig": false, "md5_digest": "c67418580f119d159212b8acfe66bf00", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 43358, "upload_time": "2015-12-05T21:24:06", "url": "https://files.pythonhosted.org/packages/dc/00/bf4fe803a6346b75340727423d9793c12de429de55812bf1dabe7baffe7c/hubward-0.2.1.tar.gz" } ], "0.2.2": [ { "comment_text": "", "digests": { "md5": "335a36f6eb5e38bfb5f9d0f518aba2f7", "sha256": "7cbe33f93ac8866fe0846109903123c7913300a93b62c4431ff2e70a7d9e06d8" }, "downloads": -1, "filename": "hubward-0.2.2.tar.gz", "has_sig": false, "md5_digest": "335a36f6eb5e38bfb5f9d0f518aba2f7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 44444, "upload_time": "2016-01-20T23:05:54", "url": "https://files.pythonhosted.org/packages/15/d5/91ebc34614d20dc85c8faf40ad02374899b0e51dcce515ae959d04009833/hubward-0.2.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "335a36f6eb5e38bfb5f9d0f518aba2f7", "sha256": "7cbe33f93ac8866fe0846109903123c7913300a93b62c4431ff2e70a7d9e06d8" }, "downloads": -1, "filename": "hubward-0.2.2.tar.gz", "has_sig": false, "md5_digest": "335a36f6eb5e38bfb5f9d0f518aba2f7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 44444, "upload_time": "2016-01-20T23:05:54", "url": "https://files.pythonhosted.org/packages/15/d5/91ebc34614d20dc85c8faf40ad02374899b0e51dcce515ae959d04009833/hubward-0.2.2.tar.gz" } ] }