Mercurial > repos > sanbi-uwc > confil
comparison confil.egg-info/PKG-INFO @ 4:eaf51f9aff10 draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
author | sanbi-uwc |
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date | Mon, 04 Mar 2019 03:28:57 -0500 |
parents | |
children | 96c8c5cada47 |
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3:53a61865e86e | 4:eaf51f9aff10 |
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1 Metadata-Version: 1.0 | |
2 Name: confil | |
3 Version: 0.1.2.dev20190304 | |
4 Summary: Contamination filter | |
5 Home-page: https://github.com/COMBAT-TB/confil | |
6 Author: UNKNOWN | |
7 Author-email: UNKNOWN | |
8 License: UNKNOWN | |
9 Description-Content-Type: text/markdown | |
10 Description: # confil | |
11 | |
12 [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil) | |
13 [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil) | |
14 | |
15 :no_entry_sign: :construction: **For in-house use** | |
16 | |
17 `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff. | |
18 | |
19 ## Requirements | |
20 | |
21 - kraken2 | |
22 | |
23 ## Up and running | |
24 | |
25 ```sh | |
26 $ git clone https://github.com/COMBAT-TB/confil.git | |
27 ... | |
28 $ cd confil | |
29 $ virtualenv envname | |
30 $ source envname/bin/activate | |
31 $ pip install -r requirements.txt | |
32 $ python setup.py install | |
33 $ confil --help | |
34 $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq | |
35 ``` | |
36 | |
37 Keywords: contamination,filter | |
38 Platform: UNKNOWN |