antunderwood

module AdminFormHelper

  ##
  # All helpers related to form.
  #

  def build_form(fields = @item_fields)
    returning(String.new) do |html|
      html << "#{error_messages_for :item, :header_tag => "h3"}"
      html << "<ul>"

antunderwood

#!/bin/sh -e
### BEGIN INIT INFO
# Provides:          starling
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: Start/stop starling server
### END INIT INFO
#
# starling		This init.d script is used to start starling.
#			It basically just calls starling.

antunderwood

# http://gist.github.com/10524
# Prevents autotest from running your entire test suite after fixing a failed test.
# Works with ZenTest 3.10.0
# Place this in your .autotest file:

require 'rubygems'
require 'active_support'
class Autotest
  def run_with_not_rerunning_everything
    hook :initialize

antunderwood

# RAILSLOVE.com template
#
# with help and ideas from:
# http://gist.github.com/33337 By Peter Cooper
# http://github.com/jeremymcanally/rails-templates/tree/master/suspenders.rb Suspenders by Thoughtbot  Nathan Esquenazi


if yes?("symlink local rails copy to vendor?")
  path = ask("what's the directory of your local rails copy?")
  inside('vendor') { run "ln -s #{path} rails" }

antunderwood

# Filters added to this controller apply to all controllers in the application.
# Likewise, all the methods added will be available for all controllers.

class ApplicationController < ActionController::Base
  include Clearance::Authentication
  helper :all # include all helpers, all the time
  protect_from_forgery # See ActionController::RequestForgeryProtection for details

  # Scrub sensitive parameters from your log
  filter_parameter_logging :password

antunderwood

class User < ActiveRecord::Base
include Roleify::RoleifyableModel
  include Clearance::User
  
  attr_accessible :username
  
  validates_presence_of :username
  validates_uniqueness_of :username
  
  def self.authenticate(email, password)

antunderwood

# Splits up alignemnt into block sized chunks and then render them as html
class RenderAlignment < CloudCrowd::Action
  require 'rubygems'
  require 'bio'
  # Split up alignment
  def split
    fasta_sequences = Bio::FlatFile.open(input_path).to_a
    alignment = Bio::Alignment.new(fasta_sequences)
    block_size = options['block_size']
    number_of_blocks = (alignment.alignment_length/block_size.to_f).ceil

antunderwood

# Author:: Anthony Underwood
# Date:: 2008-07-04

require 'rubygems'
require 'bio'

# Method to perform a remote blast
# input:: a sequence object , a string specifiying the program (blastn, blastp, blastx etc), a remote database (e.g nr-nt for non-redundant) and options (e.g -e 0.0001)
# output:: a  Bio::Blast::Report object
def remote_blast(seq_obj, program, db = 'nr-nt', options = '', server = 'genomenet')

antunderwood

number_of_strains = 500
k = 900 # number of variant sites in the alignment, i.e all non-consrved columns
harmonic_number = (1...number_of_strains).inject{|sum, n| sum + 1.0/n} # note ... so that this will calculate harmonic of n-1

theta = k/harmonic_number

antunderwood

[passenger@s0 ~]$ rvm --trace install 1.9.2  -C --with-openssl-dir=$HOME/.rvm/usr
+ [[ -z '' ]]
+ export 'PS4=+${BASH_SOURCE} : ${LINENO} : ${FUNCNAME[0]:+${FUNCNAME[0]}() : }'
+ PS4='+${BASH_SOURCE} : ${LINENO} : ${FUNCNAME[0]:+${FUNCNAME[0]}() : }'
+/home/passenger/.rvm/scripts/cli : 568 : __rvm_parse_args() : [[ -z '' ]]
+/home/passenger/.rvm/scripts/cli : 568 : __rvm_parse_args() : [[ -n '' ]]
+/home/passenger/.rvm/scripts/cli : 570 : __rvm_parse_args() : [[ 0 -eq 1 ]]
+/home/passenger/.rvm/scripts/cli : 570 : __rvm_parse_args() : [[ -n '' ]]
+/home/passenger/.rvm/scripts/cli : 14 : __rvm_parse_args() : [[ -n install ]]
+/home/passenger/.rvm/scripts/cli : 15 : __rvm_parse_args() : rvm_token=install