Mercurial > repos > sanbi-uwc > confil

annotate confil.egg-info/PKG-INFO @ 4:eaf51f9aff10 draft

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planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
author sanbi-uwc
date Mon, 04 Mar 2019 03:28:57 -0500
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children 96c8c5cada47
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eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
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1 Metadata-Version: 1.0
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2 Name: confil
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3 Version: 0.1.2.dev20190304
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4 Summary: Contamination filter
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5 Home-page: https://github.com/COMBAT-TB/confil
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6 Author: UNKNOWN
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7 Author-email: UNKNOWN
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8 License: UNKNOWN
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9 Description-Content-Type: text/markdown
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10 Description: # confil
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12 [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
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13 [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil)
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15 :no_entry_sign: :construction: **For in-house use**
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17 `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff.
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19 ## Requirements
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21 - kraken2
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23 ## Up and running
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25 ```sh
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26 $ git clone https://github.com/COMBAT-TB/confil.git
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27 ...
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28 $ cd confil
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29 $ virtualenv envname
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30 $ source envname/bin/activate
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31 $ pip install -r requirements.txt
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32 $ python setup.py install
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33 $ confil --help
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34 $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq
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35 ```
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37 Keywords: contamination,filter
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38 Platform: UNKNOWN