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        "author": "SANBI",
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        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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        "description": "# **tbvcfreport**\n\n[![Build Status](https://travis-ci.org/COMBAT-TB/tbvcfreport.svg?branch=master)](https://travis-ci.org/COMBAT-TB/tbvcfreport)\n[![Anaconda-Server Badge](https://anaconda.org/thoba/tbvcfreport/badges/version.svg)](https://anaconda.org/thoba/tbvcfreport)\n\nA tool to generate an interactive HTML-based report from SnpEff annotated VCF file(s) with links to the Combat-TB-Explorer.\n\n![test-report-img](img/test-report.png)\n\n## Usage\n\n**Prerequisites:**\n\n- `python-pip`\n- [SnpEff](http://snpeff.sourceforge.net/SnpEff_manual.html) annotated *M.tuberculosis* VCF file(s).\n- A [Combat-TB-NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) instance, `tbvcfreport` defaults to [neodb.sanbi.ac.za](https://neodb.sanbi.ac.za).\n  - See [combat-tb-neodb](https://github.com/COMBAT-TB/combat-tb-neodb) if you want a local installation and `export DATABASE_URI=localhost` for `tbvcfreport` to use your local instance.\n\n### Installation\n\n#### Using `pip`\n\n```sh\n$ pip install -i https://test.pypi.org/simple/ tbvcfreport\n...\n```\n\n#### From source\n\n```sh\n$ git clone https://github.com/COMBAT-TB/tbvcfreport.git\n...\n$ cd tbvcfreport\n$ virtualenv envname\n$ source envname/bin/activate\n$ pip install -r requirements.txt\n$ pip install -e .\n```\n\n### Run `tbvcfreport`\n\n```sh\n$ tbvcfreport --help\nUsage: tbvcfreport [OPTIONS] COMMAND [ARGS]...\n\n  Generate an HTML-based VCF report from SnpEff annotated VCF file(s).\n\nOptions:\n  --help  Show this message and exit.\n\nCommands:\n  generate  Generate an interactive HTML-based VCF report.\n\n```\n\n```sh\n$ tbvcfreport generate --help\nUsage: tbvcfreport generate [OPTIONS] VCF_DIR\n\n  Generate an interactive HTML-based VCF report.\n\nOptions:\n  -t, --tbprofiler-report FILENAME\n                                  TBProfiler json report.\n  -f, --filter-udi / -nf, --no-filter-udi\n                                  Filter upstream, downstream and intergenic\n                                  variants.  [default: True]\n  --help                          Show this message and exit.\n\n```\n\n```sh\n$ tbvcfreport generate VCF_DIR/\nProcessing...\n```\n\nThis will generate a `{vcf-file-name}.html` file in the current working directory (`pwd`).\n\n## In Galaxy\n\n:construction:\n\nWe have also added `tbvcfreport` to the [Galaxy](https://github.com/galaxyproject) [Test Tool Shed](https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0f42e4f01e64b182).\n\nKindly see [`this repository`](https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0f42e4f01e64b182) for the latest revision.\n\n![Galaxy-tbvcfreport](img/tbvcfreport.png)",
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