require 'rbconfig'
require 'open-uri'
require 'fileutils'
include FileUtils::Verbose
require 'rake/clean'

URL = "http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download"

task :download do
  open(URL) do |uri|
    File.open("samtools-0.1.19.tar.bz2",'wb') do |fout|
      fout.write(uri.read)
    end #fout 
  end #uri
end
    
task :compile do
  sh "tar xvfj samtools-0.1.19.tar.bz2"
  cd("samtools-0.1.19") do
    sh "patch < ../Makefile-bioruby.patch"
    # This patch replace CURSES lib with NCURSES which it is the only one available in OpenSUSE
    sh "patch < ../Makefile-suse.patch"
    case Config::CONFIG['host_os']
      when /linux/
        #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
        sh "make"
        cp("libbam.a","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
        #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
        sh "make libbam.so.1-local"
        cp("samtools", "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
        cp("libbam.so.1","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
      when /darwin/
        sh "make"
        cp("libbam.a","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
        sh "make libbam.1.dylib-local"
        cp("libbam.1.dylib","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
        sh "make"
        cp('samtools', "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")      
      when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"  
    end #case
  end #cd
  cd("samtools-0.1.19/bcftools") do
    sh "make"
    cp('bcftools', "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
  end
end
  
task :clean do
  cd("samtools-0.1.19") do
    sh "make clean"
  end
  rm("samtools-0.1.19.tar.bz2")
  rm_rf("samtools-0.1.19")
end

task :default => [:download, :compile, :clean]