Steve Moss gawbul

## .bash_profile
#  ---------------------------------------------------------------------------
#
#  Description:  This file holds all my BASH configurations and aliases.
#                Much of this was originally copied from:
#                http://natelandau.com/my-mac-osx-bash_profile/
#
#  Sections:
#  1.   Environment Configuration
#  2.   Make Terminal Better (remapping defaults and adding functionality)
#  3.   File and Folder Management

## chef-shell-kitchen.txt
cd /tmp/kitchen.
/opt/chef/embedded/bin/gem install chef-zero
/opt/chef/embedded/bin/chef-zero -d
knife cookbook upload -a -c solo.rb
knife environment from file environments/DEV.json -c solo.rb
chef-shell -z -c solo.rb -o '<YOUR RECIPE>'

## openconnect.md

      
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                gawbul
                / openconnect.md
            
            
              Created
              December 22, 2015 08:48
                — forked from moklett/openconnect.md
            
              
                OpenConnect VPN on Mac OS X
              
          
    Unfortunately, the Cisco AnyConnect client for Mac conflicts with Pow. And by "conflicts", I mean it causes a grey-screen-of-death kernel panic anytime you connect to the VPN and Pow is installed.
As an alternative, there is OpenConnect, a command-line client for Cisco's AnyConnect SSL VPN.
Here's how to get it set up on Mac OS X:


OpenConnect can be installed via homebrew:
 brew update


brew install openconnect

  
## roll_ipython_in_aws.md

      
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                gawbul
                / roll_ipython_in_aws.md
            
            
              Created
              March 31, 2013 20:39
                — forked from iamatypeofwalrus/roll_ipython_in_aws.md
            
              
                Roll your own IPython Notebook Server with AWS
              
          
    What

Roll your own iPython Notebook server with Amazon Web Services (EC2) using their Free Tier.
What are we using? What do you need?


An active AWS account. First time sign-ups are eligible for the free tier for a year
One Micro Tier EC2 Instance
With AWS we will use the stock Ubuntu Server AMI and customize it.
Anaconda for Python.
Coffee/Beer/Time


## GPL.md

      
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                gawbul
                / GPL.md
            
            
              Created
              January 14, 2013 18:22
                — forked from jnrbsn/GPL.md
            
              
                GNU GPLv3 in Markdown
              
          
    GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license
document, but changing it is not allowed.

  
## parallelPAML.py
#!/usr/bin/python
'''
Launch codeml on all the alignments

Marco Galardini 2012
University of Florence
GPL v3.0
'''
from optparse import OptionParser, OptionGroup
from time import strftime

## query_cite.rb
#!/usr/bin/ruby
require 'sqlite3'

cite_part = ARGV[0]
db_name = "/Users/nernst/Library/Application\ Support/Mendeley\ Desktop/neil\@neilernst.net\@www.mendeley.com.sqlite"
db = SQLite3::Database.new( db_name )
db.results_as_hash = true
query = "select citationkey, title, year from Documents where citationkey like '%#{cite_part}%'"#MATCH '#{cite_part}'"#{}like '%#{cite_part}%'"
db.execute( query ) do |row|
  print row['citationKey'] + '|'
	# ---------------------------------------------------------------------------
	#
	# Description: This file holds all my BASH configurations and aliases.
	# Much of this was originally copied from:
	# http://natelandau.com/my-mac-osx-bash_profile/
	#
	# Sections:
	# 1. Environment Configuration
	# 2. Make Terminal Better (remapping defaults and adding functionality)
	# 3. File and Folder Management
	cd /tmp/kitchen.
	/opt/chef/embedded/bin/gem install chef-zero
	/opt/chef/embedded/bin/chef-zero -d
	knife cookbook upload -a -c solo.rb
	knife environment from file environments/DEV.json -c solo.rb
	chef-shell -z -c solo.rb -o '<YOUR RECIPE>'
	#!/usr/bin/python
	'''
	Launch codeml on all the alignments

	Marco Galardini 2012
	University of Florence
	GPL v3.0
	'''
	from optparse import OptionParser, OptionGroup
	from time import strftime
	#!/usr/bin/ruby
	require 'sqlite3'

	cite_part = ARGV[0]
	db_name = "/Users/nernst/Library/Application\ Support/Mendeley\ Desktop/neil\@neilernst.net\@www.mendeley.com.sqlite"
	db = SQLite3::Database.new( db_name )
	db.results_as_hash = true
	query = "select citationkey, title, year from Documents where citationkey like '%#{cite_part}%'"#MATCH '#{cite_part}'"#{}like '%#{cite_part}%'"
	db.execute( query ) do \|row\|
	print row['citationKey'] + '\|'