Rakefile.iop_connections

require 'rubygems'
require 'fileutils'
require 'rake/clean'


###
# fetch the data 
desc "Fetch collaboration data"
file 'collaborations.xls' do
  sh "wget -O collaborations.xls 'http://github.com/cassj/my_bioinfo_scripts/raw/master/collaborations.xls'"
end

CLOBBER.include('collaborations.xls')
CLEAN.include('collaborations.xls')


###
# fetch the required scripts
###
desc "Fetch convert_excel.pl"
file 'convert_excel.pl' do
  sh "wget -O convert_excel.pl  'http://github.com/cassj/my_bioinfo_scripts/raw/master/convert_excel.pl'"
end

desc "draw_iop_collaborations.R"
file 'draw_iop_collaborations.R' do
  sh "wget -O draw_iop_collaborations.R  'http://github.com/cassj/my_bioinfo_scripts/raw/master/draw_iop_collaborations.R'"
end

desc "Fetch all required scripts"
task :fetch_all_scripts => ['convert_excel.pl','draw_iop_collaborations.R'] do
end

CLEAN.include('convert_excel.pl')
CLEAN.include('draw_iop_collaborations.R')

CLOBBER.include('convert_excel.pl')
CLOBBER.include('draw_iop_collaborations.R')



###
# Convert excel file to csv
###
desc "Convert excel to csv"
task :excel2csv => ['collaborations.xls', 'convert_excel.pl'] do
  sh "perl convert_excel.pl collaborations.xls"
end

CLEAN.include("*.csv")
CLOBBER.include("*.csv")


###
#  Generate pdf graphic
###
desc "Make PDF Plot"
file "collaboration.pdf" => ['excel2csv','draw_iop_collaborations.R' ] do
   sh "R --vanilla --slave< draw_iop_collaborations.R"
end

CLOBBER.include("collaboration.pdf")


###
# Do everything by default.
###
task :default => ['collaboration.pdf']