#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

• http://0.0.0.0:4569/sources/bam
• http://0.0.0.0:4569/sources/vcf

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

• http://0.0.0.0:4569/json/bam/hg.18?min=1&max=10000&segment=22

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

• http://0.0.0.0:4569/json/vcf/genotypes.vcf.gz?segment=1&min=1073361&max=1238825

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