ClipCrop Installation on Linux Mint 16 nvm, Node, npm Included

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ClipCrop is a tool for detecting structural variations from SAM files. And it’s built with Node.js.

ClipCrop uses two softwares internally so they should be installed first.

Install SHRiMP2

SHRiMP is a software package for aligning genomic reads against a target genome.

$ mkdir ~/software
$ cd ~/software 
$ wget
$ tar xzvf SHRiMP_2_2_3.lx26.x86_64.tar.gz
$ cd SHRiMP_2_2_3
$ file bin/gmapper

Install BWA

BWA is a software package for mapping low-divergent sequences against a large reference genome.

BWA requires zlib so install it first

$ sudo apt-get install zlib1g-dev

Download latest BWA software from SourceForge

$ cd ~/Downloads
$ tar xjvf bwa-0.7.7.tar.bz2
$ cd bwa-0.7.7
$ make
$ sudo mv ~/Downloads/bwa-0.7.7 /usr/local/bin
$ sudo ln -s /usr/local/bin/bwa-0.7.7 /usr/local/bin/bwa
$ sudo nano /etc/profile

Copy-paste this at the end the document


Save it pressing CTRL + X, then Y and hit ENTER

Now, NVM and Node should be installed but before there are some dependencies.

$ sudo apt-get install build-essential
$ sudo apt-get install libssl-dev curl

Install NVM

NVM is Node Version Manager and allows you to use different versions of Node.js

$ git clone git:// ~/.nvm
$ source ~/.nvm/
$ nvm install v0.6.1
$ nvm use v0.6.1
Now using node v0.6.1 

This installation also sets up Node.js v0.6.1, check:

$ node -v

To install ClipCrop we need one last thing which is NPM - Node Package Manager.

Install NPM

$ sudo apt-get install -y python-software-properties python g++ make
$ sudo add-apt-repository ppa:richarvey/nodejs
$ sudo apt-get update
$ sudo apt-get install nodejs npm
$ node -v

This last step will also install a Node.js version but before using ClipCrop, using NVM, Node.js version will be set to v0.6.1 like this:

$ nvm use v0.6.1
Now using node v0.6.1 

If it says No command 'nvm' found:

$ source ~/.nvm/

Install ClipCrop

$ cd ~ 
$ npm install clipcrop
$ cd ~/node_modules/clipcrop
$ npm link


$ clipcrop

This will tell you how to use the package and what options it has. More is available here.

Some pages to refer

Installation notes for BWA version 0.7.5a-r405,

Installing Node.js using NVM on Ubuntu,

How to install node.js and npm in ubuntu or mint,

Installing Node.js via package manager,

npm documentation,

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