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https://github.com/alexpreynolds/tabix-service

A nodejs-based service for requests for tabix-indexed genomic data

https://github.com/alexpreynolds/tabix-service

Science Score: 13.0%

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Keywords

bioinformatics genomics genomics-visualization nodejs samtools tabix web-service
Last synced: 5 months ago · JSON representation

Repository

A nodejs-based service for requests for tabix-indexed genomic data

Basic Info
  • Host: GitHub
  • Owner: alexpreynolds
  • License: mit
  • Language: JavaScript
  • Default Branch: master
  • Size: 124 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 4
  • Open Issues: 1
  • Releases: 0
Topics
bioinformatics genomics genomics-visualization nodejs samtools tabix web-service
Created over 8 years ago · Last pushed over 6 years ago
Metadata Files
Readme License

README.md

tabix-service

A nodejs-based service for requests for tabix-indexed genomic data

Prerequisites

These instructions assume a CentOS 7 host and sudo-level access. It's probably easiest to set up a virtual host and run these tests within that host.

htslib toolkit

To set up htslib (and bgzip and tabix tools):

$ git clone git://github.com/samtools/htslib.git $ git clone git://github.com/samtools/bcftools.git $ sudo yum install zlib-devel $ sudo yum install bzip2-devel $ sudo yum install xz-devel $ sudo yum install curl-devel $ cd bcftools $ make $ sudo make install $ cd ../htslib $ make $ sudo make install

This should put bgzip and tabix into /usr/local/bin.

Compressing and indexing test intervals

Compress and index the test interval file sample.bed, if not already done:

$ bgzip sample.bed $ tabix -p bed sample.bed.gz

This creates two files: sample.bed.gz and sample.bed.gz.tbi.

A test query would work like this:

$ tabix sample.bed.gz chr1:10000000-11000000 chr1 10037856 10038006 id-501897 102 chr1 10197056 10197206 id-509857 19

Node.js

To install Node.js:

$ sudo yum install epel-release $ sudo yum install nodejs $ sudo yum install npm

Tabix server and client

Install the Node.js dependencies, if not installed:

$ cd tabix-service/server $ npm install $ cd ../client $ npm install

Starting Tabix service

$ cd tabix-service/server $ export TABIX_SERVER_PORT=1234 $ node app.js

Starting Tabix test client

$ cd tabix-service/client $ export TABIX_CLIENT_PORT=4567 $ node app.js

Then visit http://localhost:4567 to run test queries.

tabixservicesnapshot

Owner

  • Name: Alex Reynolds
  • Login: alexpreynolds
  • Kind: user
  • Location: Seattle, WA USA
  • Company: Altius Institute for Biomedical Sciences

Pug caregiver, curler, cyclist, gardener, beginning French scholar

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Dependencies

client/package.json npm
  • express ^4.15.3
  • jquery ^3.2.1
  • path ^0.12.7
  • request ^2.81.0
  • winston ^2.3.1
server/package.json npm
  • child_process ^1.0.2
  • express ^4.15.3
  • fs 0.0.1-security
  • http 0.0.0
  • path ^0.12.7
  • request ^2.81.0
  • url ^0.11.0
  • valid-url ^1.0.9
  • winston ^2.3.1