sb2nhri Files

=How to run=

1, run with VirtualBox or VMware
	Use VirtualBox(https://www.virtualbox.org/) or VMware(http://www.vmware.com/tw) to import drVM.ova. 
	$ unzip drVM.zip
	
2, run with Docker
	Use docker to pull docker image and run.
	$ docker pull 990210oliver/drvm
	$ docker run [options] 990210oliver/drvm /bin/bash
			
3, install drVM (Tools.zip)
	To install all related tools, and use python scripts to run.
			
	-Installation-
	Use ubuntu 14.04 as OS to show how to install.
			
	* python 2.7
		apt-get install python2.7 python2.7-dev
	* python package
		apt-get install build-essential python-dev python-numpy python-scipy libatlas-dev libatlas3gf-base python-matplotlib libatlas-base-dev
	* blastn, g++	and some toolkits
		apt-get install g++
		apt-get install ncbi-blast*
		apt-get install wget dos2unix unzip
	* bz2file
		/Tools/bz2file-0.98
		python setup.py install
	* screed
		/Tools/screed-0.9
		python setup.py install
	* setuptools
		/Tools/setuptools-3.4.3
		python setup.py install
	* khmer
		/Tools/khmer-2.0
		python setup.py install
	* set PATH
		export PATH=$PATH:/Tools:/Tools/snap-0.15.4-linux:/Tools/SPAdes-3.6.1-Linux/bin:/Tools/soap2.21release:/Tools/sratoolkit.2.5.4-1-ubuntu64/bin

=Run drVM.py=

$ drVM.py -h
	Usage:
	drVM.py -1 read1.fastq -2 read2.fastq [options]
	Options:
	-type iontorrent [default: illumina]
	-dn off [digital normalization. default: on]
	-t <int> [number of threads, default: 2]
	-md <int> [min depth, default: 1]
	-ar <float> [alignment rate, default: 0.5 (0.1~0.9)]
	-bi <int> [blast identity, default: 80 (50~100)]
	-cl <int> [contig length, to keep assembly, default: 3000]
	
=Output=
	myOutput_YYYYMMDD_HHMM
	1, All genus level fastq file.
	2, Virus coverage profile pdf file. 
	3, Virus contig fasta file.
	4, Genus coverage summary file.
	5, log file.

Date: 2017/05/26
Author: Yu-Chieh Liao (jade@nhri.org.tw) and Hsin-Hung Lin (oliver0618@nhri.org.tw)
This work has been published in GigaScience 2017.
https://academic.oup.com/gigascience/article/2929394/

License: GNU General Public License, version 3.0 (GPL-3.0)