ngs_server 0.1 → 0.2

data/bin/ngs_server

@@ -1,58 +1,80 @@
 #!/usr/bin/env ruby
+  require 'optparse'
+  
+  path = File.dirname(__FILE__)
+  
+  $:.unshift File.join(path, "../lib")
 
-command = ARGV[0]
-path = `which ngs_server`
-
-puts Dir.pwd
-`ls ext/bamtools/binw`
-
-if command == 'start'
-  require 'rubygems'
-  require 'sinatra'
-  require 'json'
-
-  set :public, '.'
-  set :port, "4569"
-
-  bamtools_path = "ext/bamtools/bin/bamtools"
-  vcftools_path = "~/Tools/vcftools_0.1.7/bin/vcf-query"
-
-
-  get '/json/bam/*' do |path|
-
-    content_type :json
-    response['Access-Control-Allow-Origin'] = '*';
-
-    # invoke with eg: base_url/json/bam/file=subset22-sorted.bam?min=30000000&max=30010000&segment=22   
-    json = `#{bamtools_path} convert -in data/#{path} -format json -region #{params["segment"]}:#{params["min"]}..#{params["max"]}`
-    json       
-
-  end
-
-  get '/json/vcf/*' do |path|
-
-    content_type :json
-    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
-    json = `#{vcftools_path} data/#{path} #{params["segment"]}:#{params["min"]}-#{params["max"]} -f '{"reference":"%CHROM","position":%POS,"ref":"%REF","alt":"%ALT","info":%INFO},'`
-    json
-
-  end
-
-  get '/json/sources/:extension' do
-
-    content_type :json
-    response['Access-Control-Allow-Origin'] = '*';
+  require 'Ngs_server'
+  
 
-    # invoke with eg: base_url/json/vcf/file=ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
-    list = `find -L data -name *#{params['extension']} | awk -F/ '{ for(i=2; i<NF; i++) {printf("%s/", $i)} print $NF }'`
-    list
+  require 'ngs_server/version'
+  require 'ngs_server/add'
+  
 
+  options = {}
+  command = ""
+
+  optparse = OptionParser.new do |opts|
+    opts.banner = "Usage: ngs_server start|stop|add [options]"
+    
+    opts.on( '-h', '--help', 'display this screen' ) do
+        # puts "ngs_server command options"
+        # puts "ngs_server start"
+        
+        puts opts
+        puts "Examples:"
+        puts "\tngs_server start"
+        puts "\tngs_server start -p 4567 -d"
+        puts "\tngs_server add path_to_data_directory"
+        puts "\tngs_server stop"
+        exit
+    end
+    
+    options[:port] = '4569'    
+    opts.on( '-p', '--port PORT', 'specifies to port to listen on' ) do |f|
+        options[:port] = f
+    end
+    
+    options[:daemonize] = ""
+    opts.on( '-d', '--daemonize', 'runs process in the background' ) do
+        options[:daemonize] = "-d";
+    end
+    
+    # opts.on( '-C', '--config', 'configuration file for Thin server' ) do |f|
+    #     options[:config] = f;
+    # end
+    
   end
-
   
-elsif command == 'add-data'
+  optparse.parse!
+  command = ARGV[0]
   
   
-end
+
+  if (command == 'start')
+   # ngsrun options
+   rackup_path = File.join(path, '../lib/config.ru')
+   puts ">> NGS web server (version " + NgsServer::VERSION + ")"
+   if (options[:daemonize] == '-d')
+     puts ">> Listening on 0.0.0.0:" + options[:port]
+   else
+     puts ">> Listening on 0.0.0.0:" + options[:port] + ", CTRL+C to stop"
+   end
+   `thin -R #{rackup_path} -p #{options[:port]} #{options[:daemonize]} start`
+
+   #NgsServer.run!
+  elsif (command == 'stop')
+    rackup_path = File.join(path, '../lib/config.ru')
+    `thin -R #{rackup_path} -p #{options[:port]} stop`
+  elsif (command == 'add')
+    # source_path = File.absolute_path(ARGV[1])
+    # puts source_path
+    # file_name = File.basename(source_path)
+    # puts file_name
+    # data_dir_path = File.join(path,'../data', file_name)
+    # puts data_dir_path
+    # `ln -s #{source_path} #{data_dir_path}`
+    ngsadd ARGV[1]
+  end
+  

data/ext/bamtools/extconf.rb

@@ -2,8 +2,8 @@
 #dir = Dir.pwd
 
 #Dir.chdir("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/build")
-if !File.directory? "bin"
-  `cmake .`
-end
+
+`cmake .`
+
 
 #Dir.chdir(dir)

data/ext/vcftools/Makefile

@@ -0,0 +1,28 @@
+#
+# 1) Compiling
+#   Type make in this directory
+#
+# 2) Installation
+#   Edit the BINDIR and MODDIR below as necessary or pass the PREFIX variable
+#   to the make command. When not set, the programs will be placed in "bin" 
+#   and "lib" subdirectories in this directory.
+#       PREFIX="/install/to/path/prefix" make install
+#
+#   Add the MODDIR to your PERL5LIB environment variable:
+#       export PERL5LIB=${PREFIX}/lib:${PERL5LIB}
+#
+
+
+ifndef PREFIX
+    export PREFIX = $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
+endif
+export BINDIR = ${PREFIX}/bin
+export MODDIR = ${PREFIX}/lib
+
+DIRS = cpp perl
+install:
+	    @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
+        for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
+
+clean:
+		@for dir in $(DIRS); do cd $$dir && $(MAKE) clean && cd ..; done

data/ext/vcftools/README.txt

@@ -0,0 +1,36 @@
+License:
+    The program package is released under the GNU General Public License
+    version 3.0 (GPLv3).
+
+Credits:
+    Adam Auton   (cpp)
+    Petr Danecek (perl)
+    
+Compiling:
+    To compile and install VCFtools, you should type 'make' in the 
+    vcftools folder. The perl scripts and cpp executable will be 
+    installed in the /vcftools_(version_num)/bin/ folder. It is 
+    recommended that you add this folder to you PATH.
+
+Documentation:
+    The latest version of the documentation and examples of usage can be 
+    found in the website subdirectory or go online:
+         http://vcftools.sourceforge.net/docs.html
+
+Getting Help:
+    The best way to get help regarding VCFtools is to email the mailing
+    list: vcftools-help@lists.sourceforge.net 
+    
+Citation:
+    If you make use of VCFtools in your research, we would appreciate a 
+    citation of the following paper:
+
+    The Variant Call Format and VCFtools, 
+    Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, 
+    Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, 
+    Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin 
+    and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
+    
+    http://dx.doi.org/10.1093/bioinformatics/btr330
+    
+    

data/ext/vcftools/cpp/.svn/all-wcprops

@@ -0,0 +1,125 @@
+K 25
+svn:wc:ra_dav:version-url
+V 34
+/svnroot/vcftools/!svn/ver/620/cpp
+END
+vcf_entry.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 48
+/svnroot/vcftools/!svn/ver/611/cpp/vcf_entry.cpp
+END
+dgeev.h
+K 25
+svn:wc:ra_dav:version-url
+V 42
+/svnroot/vcftools/!svn/ver/508/cpp/dgeev.h
+END
+vcftools.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 47
+/svnroot/vcftools/!svn/ver/620/cpp/vcftools.cpp
+END
+output_log.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 49
+/svnroot/vcftools/!svn/ver/457/cpp/output_log.cpp
+END
+parameters.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 49
+/svnroot/vcftools/!svn/ver/620/cpp/parameters.cpp
+END
+vcf_entry.h
+K 25
+svn:wc:ra_dav:version-url
+V 46
+/svnroot/vcftools/!svn/ver/546/cpp/vcf_entry.h
+END
+vcf_file_index.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/584/cpp/vcf_file_index.cpp
+END
+vcftools.h
+K 25
+svn:wc:ra_dav:version-url
+V 45
+/svnroot/vcftools/!svn/ver/259/cpp/vcftools.h
+END
+vcf_file_filters.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 55
+/svnroot/vcftools/!svn/ver/619/cpp/vcf_file_filters.cpp
+END
+vcf_file_diff.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/555/cpp/vcf_file_diff.cpp
+END
+output_log.h
+K 25
+svn:wc:ra_dav:version-url
+V 47
+/svnroot/vcftools/!svn/ver/457/cpp/output_log.h
+END
+vcf_entry_setters.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/612/cpp/vcf_entry_setters.cpp
+END
+parameters.h
+K 25
+svn:wc:ra_dav:version-url
+V 47
+/svnroot/vcftools/!svn/ver/620/cpp/parameters.h
+END
+vcf_file.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 47
+/svnroot/vcftools/!svn/ver/620/cpp/vcf_file.cpp
+END
+vcf_file.h
+K 25
+svn:wc:ra_dav:version-url
+V 45
+/svnroot/vcftools/!svn/ver/620/cpp/vcf_file.h
+END
+vcf_file_format_convert.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 62
+/svnroot/vcftools/!svn/ver/547/cpp/vcf_file_format_convert.cpp
+END
+dgeev.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 44
+/svnroot/vcftools/!svn/ver/508/cpp/dgeev.cpp
+END
+vcf_entry_getters.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/612/cpp/vcf_entry_getters.cpp
+END
+Makefile
+K 25
+svn:wc:ra_dav:version-url
+V 43
+/svnroot/vcftools/!svn/ver/575/cpp/Makefile
+END
+vcf_file_output.cpp
+K 25
+svn:wc:ra_dav:version-url
+V 54
+/svnroot/vcftools/!svn/ver/620/cpp/vcf_file_output.cpp
+END

data/ext/vcftools/cpp/.svn/dir-prop-base

@@ -0,0 +1,6 @@
+K 10
+svn:ignore
+V 9
+vcftools
+
+END