Download Latest Version Tools.tar.gz (105.2 MB)
Email in envelope

Get an email when there's a new version of sb2nhri

Home / MyCC / Data
Name Modified Size InfoDownloads / Week
Parent folder
benchmark 2015-09-10
0
fly.zip 2015-12-17 40.3 MB
0
64s.zip 2015-09-11 107.5 MB
0
Sharon.zip 2015-09-11 14.9 MB
0
100s.zip 2015-09-11 187.1 MB
0
25s.zip 2015-09-11 26.0 MB
0
10s.zip 2015-09-11 18.4 MB
0
Totals: 7 Items   394.1 MB 0 
MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication. 

=How to run=

	1, MyCC.ova 
			Use VirtualBox(https://www.virtualbox.org/) or VMware(http://www.vmware.com/tw) to import MyCC.ova. 
	
	2, Docker Image 990210oliver/mycc.docker:v1
			Use docker to pull docker image and run.
			$ docker pull 990210oliver/mycc.docker:v1
			$ docker run [options] 990210oliver/mycc.docker:v1 /bin/bash
			
	
	3, 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
			* libraries
				apt-get install build-essential python-dev python-setuptoolspython-numpy python-scipy libatlas-dev libatlas3gf-base python-matplotliblibatlas-base-dev lib32stdc++6
			* scikit-learn
				/Tools/scikit-learn-0.16.0
			  python setup.py install
			* Cython
			  /Tools/Cython-0.22
			  python setup.py install
			* bhsne
				/Tools/tsne-master
			  python setup.py install
			* set PATH
				export $PATH=$PATH:/yourpath/Tools:/yourpath/Tools/fetchMG
			* edit MyCC.py
				fetchMG='/opt/fetchMG/fetchMG.pl'
				fetchMGbin='/yourpath/Tools/fetchMG/bin'
				apcluster='/yourpath/Tools/ap'
				prodigal='/yourpath/Tools/prodigal.v2_60.linux'
				uclust='/yourpath/Tools/uclustq1.2.22_i86linux64'
				cdhit='/yourpath/Tools/cd-hit/cd-hit'
				
=Run MyCC.py=

	$ MyCC.py
		Please input an assembly file.
		Usage:
		MyCC.py [inputfile] [4mer/5mer/56mer default:4mer] [Options]
		Options:
		-a A file having coverage information. 
		-t Minimum contig length. [defaults: 1000 bp]
		-lt A fraction of contigs for the first-stage clustering. [default: 0.7]
		-ct Minimum contig lengh for first stage clustering. [bp]
		-meta Change to meta mode of Prodigal. [default: single]
		-p Perplexity for BH-SNE. [default: 20, range between 5 and 50]
		-pm To set preferences all equal to the median of the other similarities for affinity propagation.
		-st Maximum distance for sparse format of affinity propagation. [default: 500]
		-mask To mask repetitive sequences.
		-keep To keep temporary files.


	For example,
	$ MyCC.py metagenomic_contigs.fasta

		
	
=Output=
		YYYYMMDD_HHMM_mer_lt folder
		1, All cluster fasta file.
		2, Cluster info file. (Cluster.summary )
		3, Sequences coordinate file. (MyCluster.coords)
		4, Cluster layout file. (MyCluster.pdf)
		5, log file.
		



Date: 2015/07/10
Author: Jade Liao (jade@nhri.org.tw) and Hsin-Hung Lin (oliver0618@nhri.org.tw)
Source: ReadMe.txt, updated 2016-01-18