=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)