gistfile1.txt

////////////////////////////The Error //////////////////////////////

unf-ubu@unf-ubu:~/rails_projects/crossbow$ ruby EMR_job.rb
http://crossbow-refs.s3.amazonaws.com/hg18.jar

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    An unexpected error has occurred.
  Please report the following lines to:
   [email protected]
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Problem: ValueError: http://crossbow-refs.s3.amazonaws.com/hg18.jar: not a recognized URI
S3cmd:   1.0.0

Traceback (most recent call last):
  File "/usr/bin/s3cmd", line 2006, in <module>
    main()
  File "/usr/bin/s3cmd", line 1950, in main
    cmd_func(args)
  File "/usr/bin/s3cmd", line 335, in cmd_object_put
    local_list, single_file_local = fetch_local_list(args)
  File "/usr/bin/s3cmd", line 237, in fetch_local_list
    uri = S3Uri(arg)
  File "/usr/share/s3cmd/S3/S3Uri.py", line 35, in __new__
    raise ValueError("%s: not a recognized URI" % string)
ValueError: http://crossbow-refs.s3.amazonaws.com/hg18.jar: not a recognized URI

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    An unexpected error has occurred.
    Please report the above lines to:
   [email protected]
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
unf-ubu@unf-ubu:~/rails_projects/crossbow$ 



///////////////////////////////////////////// THE FILE/////////////////////////////////////////////
require 'uri'

# http://localhost:3000/users/sign_in

# upload the manifest file
#s3cmd put ~/biohack/crossbow-1.1.2/example/human_g18/small.manifest s3://bg-crossbow-01/example/human_g18/small.manifest

url = URI.parse("http://crossbow-refs.s3.amazonaws.com/hg18.jar")

puts url



# sets temp env var to the EMR link
ENV["CROSSBOW_HOME"]= '/home/unf-ubu/biohack/crossbow-1.1.2/'

# sets temp env var to the EMR link
ENV["CROSSBOW_EMR_HOME"]= '/home/unf-ubu/biohack/crossbow-1.1.2/elastic-mapreduce-cli/'


upload_jar =<<END_OF_COMMAND
s3cmd put #{url} s3://bg-crossbow-01/crossbow-refs/hg18.jar
END_OF_COMMAND

# This should run the following command:
# s3cmd put http://crossbow-refs.s3.amazonaws.com/hg18.jar s3://bg-crossbow-01/crossbow-refs/hg18.jar
IO.popen(upload_jar) do |handle|
  handle.each_line do |line|
    puts line
  end
end