bionode.io

bionode-sra

A Node.js wrapper for SRA Toolkit.

Install

You need to install the latest Node.JS first, please check nodejs.org or do the following:

# Ubuntu
sudo apt-get install npm
# Mac
brew install node
# Both
npm install -g n
n stable

To use bionode-sra as a command line tool, you can install it globally with -g.

npm install bionode-sra -g

Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the node_modules directory by doing the same command without -g.

npm i bionode-sra # 'i' can be used as shortcut to 'install'

Usage

If you're using bionode-sra with Node.js, you can require the module:

var sra = require('bionode-sra')
var fastqDump = sra('fastq-dump')
fastqDump('SRR1509835.sra')

Please read the documentation for the methods exposed by bionode.

Command line examples

$ bionode-sra fastq-dump SRR1509835.sra
$ bionode-sra fastq-dump SRR1509835.sra fastqOutputDirectory

Documentation

Check our documentation at doc.bionode.io or do:

bionode-sra --help

Contributing

We welcome all kinds of contributions at all levels of experience, please read the CONTRIBUTING.md to get started!

Communication channels

Don't be shy! Come talk to us 😃

• Email [email protected]
• Chat room http://gitter.im/bionode/bionode
• IRC #bionode on Freenode
• Twitter @bionode