Project

ngs_server

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"Converts BAM/VCF files into JSON for consumption by web apps"
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 Popularity
Downloads
32,778
Stars
7
Forks
1
Watchers
4
 Releases
Current version
0.8
Total releases
10
First release
2011-12-11
Latest release
2012-06-04
 Development
Primary Language
C++
Average date of last 50 commits
2011-12-23
Reverse Dependencies
0

 Dependencies

Runtime

rack
>= 1
sinatra
>= 1.2
thin
>= 1.2
 Project Readme

#Ultralightweight NGS Server

Converts BAM and VCF files to json for consumption by a web application

install for mac and linux (no windows)

  1. download and install cmake

  2. run "gem install ngs_server" in the terminal

usage

  # in terminal
  ngs_server --help
  
  # add data directories to be served
  ngs_server add path-to-dir
  
  # start server
  ngs_server start
  ngs_server start --port 3000
  # daemonize
  ngs_server start -d
  
  # stop server if daemonized
  ngs_server stop

access data

see available data sources


invoke file: hg18.bam with coordinates 1 to 100000 on chromosome 22


vcf files must be compressed with index (see tabix)
invoke file: genotypes.vcf.gz with coordinates 1073361 to 1238825 on chromosome 1

find data

find data sources that have been added

# ngs_server find <dir> <regex>
ngs_server find . *  # return everything

# return found data as link to view in Rover
ngs_server find . "*bam" -r 1:1:100000

# specify server url that ngs_server is running on
# so the correct links to sources will be generated
ngs_server find . "*bam" -r 1:1:100000 -s http://mydataserver.com

Example

# create data directory
mkdir example-data && cd example-data

# download bam file and index
wget http://bioinformatics.bc.edu/marthlab/download/small.bam
wget http://bioinformatics.bc.edu/marthlab/download/small.bam.bai

# add data directory to ngs_server to be served
cd ../
ngs_server add example-data/

# start server
ngs_server start -d

# find data
ngs_server find . "*bam"

# generate Rover url to view data
# -r chr:min:max
ngs_server find . "*bam" -r 22:14596532:14699000
# and then just paste the generate url into a browser

# to make things quicker you can open the link from
# the command line in Google Chrome (Mac only, but linux is similar)
open -a "Google Chrome" $(ngs_server find . "*bam" -r 22:14596532:14699000)

# to see the pure json that ngs_server sends
# paste following url in browser
# http://0.0.0.0:4569/json/bam/example-data/small.bam?min=14596532&max=14699000&segment=22

# stop server
ngs_server stop