https://github.com/bionode/bionode-sra

Node.js wrapper for SRA Toolkit
https://github.com/bionode/bionode-sra

bioinformatics bionode nodejs tool wrapper

Last synced: 3 months ago
JSON representation

Node.js wrapper for SRA Toolkit

• Host: GitHub
• URL: https://github.com/bionode/bionode-sra
• Owner: bionode
• License: mit
• Created: 2014-05-19T13:08:05.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2019-01-09T15:34:17.000Z (almost 6 years ago)
• Last Synced: 2024-10-05T20:16:58.095Z (3 months ago)
• Topics: bioinformatics, bionode, nodejs, tool, wrapper
• Language: JavaScript
• Homepage: bionode.io
• Size: 285 KB
• Stars: 6
• Watchers: 21
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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# bionode-sra

> A Node.js wrapper for SRA Toolkit.

[![npm](https://img.shields.io/npm/v/bionode-sra.svg?style=flat-square)](http://npmjs.org/package/bionode-sra)

[![Travis](https://img.shields.io/travis/bionode/bionode-sra.svg?style=flat-square)](https://travis-ci.org/bionode/bionode-sra)

[![Coveralls](https://img.shields.io/coveralls/bionode/bionode-sra.svg?style=flat-square)](http://coveralls.io/r/bionode/bionode-sra)

[![Dependencies](http://img.shields.io/david/bionode/bionode-sra.svg?style=flat-square)](http://david-dm.org/bionode/bionode-sra)

[![npm](https://img.shields.io/npm/dt/bionode-sra.svg?style=flat-square)](https://www.npmjs.com/package/bionode-sra)

[![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg?style=flat-square)](https://gitter.im/bionode/bionode)

## Install

You need to install the latest Node.JS first, please check [nodejs.org](http://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](http://rawgit.com/bionode/bionode-sra/master/docs/bionode-sra.html) for the methods exposed by bionode.

### Command line examples

```sh

$ bionode-sra fastq-dump SRR1509835.sra

$ bionode-sra fastq-dump SRR1509835.sra fastqOutputDirectory

```

## Documentation

Check our documentation at [doc.bionode.io](http://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](CONTRIBUTING.md) to get started!

## Communication channels

Don't be shy! Come talk to us :smiley:

* **Email** [[email protected]](mailto:[email protected])

* **Chat room** [http://gitter.im/bionode/bionode](http://gitter.im/bionode/bionode)

* **IRC** #bionode on Freenode

* **Twitter** [@bionode](http://twitter.com/@bionode)