fix readme and add to codecov

.travis.yml

@@ -5,9 +5,13 @@ addons:
     - zlib1g-dev
     - libncurses5-dev
 python:
-  - "3.4"
+  - 3.4
 sudo: false
 install:
-  - "source ./install_dependencies.sh"
+  - source ./install_dependencies.sh
+before_script:
+  - pip install codecov
 script:
-  - "python setup.py test"
+  - coverage run setup.py test
+after_success:
+  - codecov

README.md

@@ -1,10 +1,82 @@
-Circlator
-=========
-
+# Circlator
 A tool to circularize genome assemblies.
 
+[![Build Status](https://travis-ci.org/sanger-pathogens/circlator.svg?branch=master)](https://travis-ci.org/sanger-pathogens/circlator)   
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE)   
+[![status](https://img.shields.io/badge/GenomeBiology-10.1186-brightgreen.svg)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)  
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/recipes/circlator/README.html)  
+[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/circlator)  
+[![Docker Build Status](https://img.shields.io/docker/build/sangerpathogens/circlator.svg)](https://hub.docker.com/r/sangerpathogens/circlator)  
+[![Docker Pulls](https://img.shields.io/docker/pulls/sangerpathogens/circlator.svg)](https://hub.docker.com/r/sangerpathogens/circlator)  
+[![codecov](https://codecov.io/gh/sanger-pathogens/circlator/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/circlator)
+
+## Contents
+  * [Introduction](#introduction)
+  * [Installation](#installation)
+  * [Usage](#usage)
+  * [License](#license)
+  * [Feedback/Issues](#feedbackissues)
+  * [Citation](#citation)
+  * [Further Information](#further-information)
+
+## Introduction
+Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.
+
+## Installation
 For how to install Circlator, please see the [Circlator website](http://sanger-pathogens.github.io/circlator/).
 
-For how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki).
+## Usage
+```
+Usage: circlator <command> [options] <required arguments>
+
+To get minimal usage for a command use:
+circlator command
+
+To get full help for a command use one of:
+circlator command -h
+circlator command --help
+
+
+Available commands:
+
+all        Run mapreads, bam2reads, assemble, merge, clean, fixstart
+mapreads   Map reads to assembly
+bam2reads  Make reads from mapping to be reassembled
+assemble   Run assembly using reads from bam2reads
+merge      Merge original assembly and new assembly made by assemble
+clean      Remove small and completely contained contigs from assembly
+fixstart   Change start position of circular sequences
+minimus2   Run the minimus2 based circularisation pipeline
+get_dnaa   Download file of dnaA (or other of user's choice) genes
+progcheck  Checks dependencies are installed
+test       Run Circlator on a small test set
+version    Print version and exit
+```
+For more information on how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki).
+
+## License
+Circlator is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE).
+
+## Feedback/Issues
+Please report any issues to the [issues page](https://github.com/sanger-pathogens/circlator/issues) or email circlator-help@sanger.ac.uk.
+
+## Citation
+If you use this software please cite:
+
+__Circlator: automated circularization of genome assemblies using long sequencing reads__   
+Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: [10.1186/s13059-015-0849-0](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)
+
+__[BWA](http://arxiv.org/abs/1303.3997):__ Li, H et al. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997.  
+
+__[MUMmer](http://genomebiology.com/content/5/2/R12):__ Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).  
+
+__[Prodigal](http://www.biomedcentral.com/1471-2105/11/119):__ Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).  
+
+__[SAMtools](http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract):__ Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–9 (2009).  
+
+__[SPAdes](http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021)__: Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–77 (2012)  
 
-Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/circlator.svg?branch=master)](https://travis-ci.org/sanger-pathogens/circlator)
+## Further Information
+For more information on this software see:
+* the [Circlator website](http://sanger-pathogens.github.io/circlator/)
+* the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki)