Mercurial > repos > sanbi-uwc > confil

annotate confil.egg-info/PKG-INFO @ 13:bbf9ab2ebee7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
author sanbi-uwc
date Tue, 12 Mar 2019 09:16:35 -0400
parents 5ec97cccb3fe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
bbf9ab2ebee7 planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
sanbi-uwc
parents: 12
diff changeset
1 Metadata-Version: 2.1
4
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
2 Name: confil
13
bbf9ab2ebee7 planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
sanbi-uwc
parents: 12
diff changeset
3 Version: 0.1.3.dev20190307
4
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
4 Summary: Contamination filter
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
5 Home-page: https://github.com/COMBAT-TB/confil
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
6 License: UNKNOWN
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
7 Description: # confil
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
8
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
9 [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
10 [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil)
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
11
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
12 :no_entry_sign: :construction: **For in-house use**
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
13
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
14 `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff.
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
15
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
16 ## Requirements
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
17
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
18 - kraken2
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
19
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
20 ## Up and running
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
21
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
22 ```sh
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
23 $ git clone https://github.com/COMBAT-TB/confil.git
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
24 ...
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
25 $ cd confil
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
26 $ virtualenv envname
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
27 $ source envname/bin/activate
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
28 $ pip install -r requirements.txt
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
29 $ python setup.py install
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
30 $ confil --help
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
31 $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
32 ```
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
33
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
34 Keywords: contamination,filter
eaf51f9aff10 planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
sanbi-uwc
parents:
diff changeset
35 Platform: UNKNOWN
13
bbf9ab2ebee7 planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
sanbi-uwc
parents: 12
diff changeset
36 Description-Content-Type: text/markdown