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:

``bash


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.

`bash
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.

`bash
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:

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

Please read the documentation for the methods exposed by bionode.

$3


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

Documentation

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

`bash
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 :smiley:

* Email mail@bionode.io
* Chat room http://gitter.im/bionode/bionode
* IRC #bionode on Freenode
* Twitter @bionode