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bionode-sra

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bionode.io

# bionode-sra [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Coveralls Status][coveralls-image]][coveralls-url] [![Dependency Status][depstat-image]][depstat-url] [![DOI][doi-image]][doi-url]

A Node.js wrapper for SRA Toolkit.

Install

Install bionode-sra with npm:

$ npm install bionode-sra

To use it as a command line tool, you can install it globally by adding -g .

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

Contributing

To contribute, clone this repo locally and commit your code on a separate branch.

Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:

$ npm test

Please also check for code coverage:

$ npm run coverage

To rebuild the documentation using the comments in the code:

$ npm run build-docs

Check the issues for ways to contribute.

Contacts

Bruno Vieira <mail@bmpvieira.com> @bmpvieira

Yannick Wurm (yannick.poulet.org) @yannick__

License

bionode-sra is licensed under the MIT license.
Check ChooseALicense.com for details.

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