ngs_server 0.2.1 → 0.2.2

data/README.md

@@ -0,0 +1,42 @@
+#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
+      
+<br/>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
+      
+<br/>vcf files must be compressed with index (see tabix)<br/>
+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

data/bin/ngs_server

@@ -5,7 +5,7 @@
   
   $:.unshift File.join(path, "../lib")
 
-  require 'Ngs_server'
+  require 'ngs_server'
   
 
   require 'ngs_server/version'

data/lib/ngs_server/version.rb

@@ -1,3 +1,3 @@
 module NgsServer
-  VERSION = "0.2.1"
+  VERSION = "0.2.2"
 end

data/lib/ngs_server.rb

@@ -5,19 +5,17 @@ require 'sinatra/base'
 
 class MyNgsServer < Sinatra::Base
   set :server, 'thin'
-  #set :run, true
-  #set :public, '.'
- # set :port, opts[:port]
- #set :port, 4569
-#  set :daemonize, opts[:daemonize]
-#  set :daemonize, true
 
   gempath = File.join(File.dirname(__FILE__), "../")
   datapath = File.join(gempath, 'data')
   bamtools_path = "#{gempath}/ext/bamtools/bin/bamtools"
   vcftools_path = "#{gempath}/ext/vcftools/bin/vcf-query"
+  get '/test' do
 
+    'hi'
+  end
 
+  
   get '/json/bam/*' do |path|
 
     content_type :json
@@ -46,7 +44,7 @@ class MyNgsServer < Sinatra::Base
     response['Access-Control-Allow-Origin'] = '*';
 
     # invoke with eg: base_url/json/vcf/file=ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
-    list = `find -L #{datapath} -name *#{params['extension']} | awk -F/ '{ for(i=2; i<NF; i++) {printf("%s/", $i)} print $NF }'`
+    list = `find -L #{datapath} -name '*#{params['extension']}' | awk -F#{datapath}/ '{print $2}'`
     list
 
   end

data/ngs_server.gemspec

@@ -4,11 +4,11 @@ require "ngs_server/version"
 
 Gem::Specification.new do |s|
   s.name        = "ngs_server"
-  s.version     = "0.2.1"
+  s.version     = "0.2.2"
   s.platform    = Gem::Platform::RUBY
   s.authors     = ["Chase Miller"]
   s.email       = ["chmille4@gmail.com"]
-  s.homepage    = ""
+  s.homepage    = "https://github.com/chmille4/ngs_server"
   s.summary     = %q{"Ultra Lightweight NGS Data Server"}
   s.description = %q{"Converts BAM/VCF files into JSON for consumption by web apps"}
   s.add_dependency('sinatra', '>= 1.2')

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 2
-  - 1
-  version: 0.2.1
+  - 2
+  version: 0.2.2
 platform: ruby
 authors: 
 - Chase Miller
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-12-13 00:00:00 -05:00
+date: 2011-12-16 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -71,6 +71,7 @@ extra_rdoc_files: []
 files: 
 - .gitignore
 - Gemfile
+- README.md
 - Rakefile
 - bin/ngs_server
 - data/holder.txt
@@ -595,7 +596,7 @@ files:
 - lib/ngs_server/version.rb
 - ngs_server.gemspec
 has_rdoc: true
-homepage: ""
+homepage: https://github.com/chmille4/ngs_server
 licenses: []
 
 post_install_message: