Name | Modified | Size | Downloads / Week |
---|---|---|---|
Parent folder | |||
myOutput_20160420_1658 | 2016-05-04 | ||
Totals: 1 Item | 0 |
=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)