mndoci

require 'rubygems'
require_gem 'activerecord'
require '/var/www/hoosier/app/models/payment_method'

#Connect to the database
ActiveRecord::Base.establish_connection(
    :adapter  => "postgresql",
    :host     => "localhost",
    :username => "****",
    :password => "****",

mndoci

Task: Protein lookup
  Find protein structure for 1MBN
  From PDB
  Return sequence of protein

Task: Blast
  Run BLAST
  Using the protein sequence from Protein lookup task
  On uniprot
  Select all hits with e < 0.00001

mndoci

# From Euan's blog post
# http://www.ghastlyfop.com/blog/2008/12/strip-html-tags-from-string-ruby.html

require 'hpricot'

page = Hpricot("<b>some marked up <i>text</i></b>")
puts page.to_plain_text

mndoci

# Crossref Ruby oneliner
# From http://www.crossref.org/CrossTech/2008/12/and_the_doi_is.html
ruby -rubygems -e 'require "mini_exiftool";
    puts MiniExiftool.new("test.pdf")["doi"]'
10.1038/nphoton.2008.200

mndoci

# This is a simple command line tool for uploading
# and folders of files to AWS S3. You must first
# create a vaild bucket to upload to.

#!/usr/bin/env ruby
require 'rubygems'
require 'pathname'
require 'aws/s3'

include AWS::S3

mndoci

# Chemcaster example
require 'rubygems'
require 'activeresource'

class Structure < ActiveResource::Base
  self.site = 'http://chemcaster.com/collections/:collection_id'
  self.user = '[email protected]'
  self.password = 'secret'
end

mndoci

#!/usr/bin/ruby
# save as pubmed.rb and test using 'ruby pubmed.rb 19662644'
# keyword search may return > 1 record due to retmax bug
# http://github.com/bioruby/bioruby/commit/51c3223e033b2992a7bd95da282f88164406ff92
# From Neil Saunders http://gist.github.com/164994

require 'rubygems'
require 'bio'

keywords = ARGV.join(' ')

mndoci

#!/usr/local/bin ruby

# From Paulo Nuin
# Source: http://ruby.genedrift.org/?p=18

require 'rubygems'
require 'bio'

my_file = File.new(ARGV[0])
refs = my_file.readlines

mndoci

# If you use osx terminal/git this includes a couple nice features:
#   1) Minimalist colors
#   2) Stripped down CLEAN prompt
#   3) For GIT folders it will display the current branch.
# To install just copy this into the top of your ~/.bash_profile
# Based on http://www.simplisticcomplexity.com/2008/03/13/show-your-git-branch-name-in-your-prompt/

function parse_git_branch {
  git branch --no-color 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/[\1]/'
}

mndoci

#SWITCHES
#-d (cap deploy when check-in finished)
#-v (verbose, defaults to quiet)
#-m "commit message" (custom commit message)

#!/bin/bash
## options to be accepted
optstr=m:dv ## colon follows options that require an argument
while getopts $optstr var
do