_    _ _______ __  __          _____                
           | |  | |__   __|  \/  |   /\   |  __ \               
           | |__| |  | |  | \  / |  /  \  | |  | |              
           |  __  |  | |  | |\/| | / /\ \ | |  | |              
           | |  | |  | |  | |  | |/ ____ \| |__| |              
   _____   |_|_ |_|  |_|  |_|  |_/_/__  \_\_____/               
  / ____|    | |     (_)        / ____|    | | |                
 | |     __ _| |_   ___ _ __   | |     ___ | | | ___  __ _  ___ 
 | |    / _` | \ \ / / | '_ \  | |    / _ \| | |/ _ \/ _` |/ _ \
 | |___| (_| | |\ V /| | | | | | |___| (_) | | |  __/ (_| |  __/
  \_____\__,_|_| \_/ |_|_| |_|  \_____\___/|_|_|\___|\__, |\___|
                                                      __/ |     
                                                     |___/      

README

HTMAD is a software package designed as a proof of concept for the phylogenetic analysis team at Calvin College.

AUTHORS
<TODO: clean up the order of names to match the order of names on the publication>
Abigail J. Streelman
Benjamin K. Johnson
James G. Fahey
Thomas E. Wodarek
Dr. Serita M. Nelesen
Dr. John T. Wertz

CONFIGURATION FILE
	To run HTMAD in a non-interactive mode, a configuration file needs to be passed into the program at run time (see USE section). The configuration file contains flags followed by a colon and then the specified option. Below are available options for the configuration file.
	* indicates mandatory specification, all other are optional (do not include asterisks in configuration file)
	* data_location: <file location>
		Specifies the file path location of the spectra data for full and graphing runs
	flagging: <Y/N>
		option to flag spectra with less than two peaks at a low intensity with an asterisk
	flagging_value: <value>
		option to change the flagging intensity threshold from the default 10000	
	graphs: <option>
		Specifies the type of graph you want output. If not specified no graphs are produced. Enter number(s) of graph(s) desired separated by commas Valid Options:
		1.Spectra
		2.Spectra with picked peaks
		3.Spectra with color-coded peak frequencies
	graph_color: <option>
		Specifies the color for the spectra. Enter single letter color code for the color option - default black. Options include:
		r = red
		y = yellow
		g = green
		b = blue
		c = cyan
		m = magenta
		k = black
		w = white
	graph_peak_color: <option>
		Specifies the colors of picked peaks on the picked peak graphs, excluding the frequency graphs. Default red.
		graph_color options for color options
	peak_location: <file location>
		Specifies the file path location of the picked peak data for analysis and graphing runs
	peak_picking_type: <type>
		Specifies the type of peak picking you want.  Valid options:
		B - Basic
		C - Custom - you specify the options of the computation run
		O - Optimal - Calculated by the HTMAD Team for general use
	peak_picking_vals: <start>, <middle>, <first>, <second>
		Specifies the values of the peak peak picking you want.
		start = Peak picking starting x-value
		middle = Picking stringency divide
		first = First stringency
		second = Second stringency
	results_location: <file location>
		Specifies the file name in HTMAD_Data for the analysis data to be saved to. If not specified, default location will be ./HTMAD_Data/HTMAD_Run.
	* run_type: <type>
		Specifies the type of analysis run you want performed.  Valid options are:
		F - Full Run
		A - Analysis Run only (uses previously picked peaks, does not perform any graphing options)
		G - Graphing Run only (skips peak picking but requires previously picked peaks and matching spectra)
	res: <value>
		Specifies the resolution of the graph you would like between 100 and 1000.  Default of 300.
	sequence_type: <type>
		Specifies the type of sequencing you want performed
		Valid options are: V1F, V1B, V2F, V2B, V3F, V3B
	UPGMA: <Y/N>
		Whether you would like to use our algorithm for UPGMA tree generation.
	
//TODO: Specify options for graphic and analysis runs>********************************  
		

USE
To use HTMAD, please use one of the following options:
	
	For all forms of access
	cd to the directory you installed HTMAD into
	cd ./HTMAD_Dev/src
	
	Interactive mode:
	python HTMAD.py
	Follow the on-screen prompts
	
	Non-Interactive mode (Requires a configuration file (see below)
	python HTMAD.py -n <path to your configuration file>
	
	

INSTALL
To install HTMAD, please do one of the following.

On Linux:
	Please download and run the script located at: http://bitbucket.org/astreelman/htmad_dev/downloads/linuxInstallScript.sh with the following commands in a terminal window:
	
	
	cd to the directory you want to install HTMAD in
	wget http://bitbucket.org/astreelman/htmad_dev/downloads/linuxInstallScript.sh
	chmod u+x linuxInstallScript.sh
	./linuxInstallScript.sh
	
	It will ask you for your password to install some of the dependencies, so please enter it when the terminal asks for it.

On Mac:
	Please download and run the script located at: http://bitbucket.org/astreelman/htmad_dev/downloads/macInstallScript.sh by doing the following:
	
	Please install the Academic Enthought Python Distribution (http://www.enthought.com)
		You will need to register for an academic license at https://www.enthought.com/products/canopy/academic/
		After you successfully register, you will be able to download and install the Enthought Python Distribution on your Mac computer.
		Enthought is used because it simplifies the resolution of dependencies (the libraries of software we rely on for HTMAD to run on the Mac platform)
	
	Please also install Mercurial:
		Go to http://mercurial.selenic.com/downloads/ and download the mercurial for your version of Mac, then double-click on the .zip file that was downloaded, then double-click on the .mpkg in the extracted folder.  From here, please follow the on-screen prompts.
	
	Launch a Terminal window (In your LaunchPad (usually located in the taskbar at the bottom of the screen) click on "Utilities" and then on "Terminal")
		At this point, you could also drag the "Terminal" icon to your taskbar for fast access later.
	cd to the directory you want to install HTMAD in
		If you don't know, you can just install it on your desktop, so use the command "cd ~/Desktop" (without quotes)
	wget http://bitbucket.org/astreelman/htmad_dev/downloads/macInstallScript.sh
	chmod u+x macInstallScript.sh
	./macInstallScript.sh

On Windows:
	We currently do not support the Windows platform, but please feel free to install the virtual machine (VM) with HTMAD installed using the instructions below.

Using a Virtual Machine (VM):
	This VM is pre-configured to run HTMAD out of the box.  You can use this VM in VirtualBox or VMWare Player (both free), just do the following:

	If you don't have VMWare Player(http://www.vmware.com/products/player/) or VirtualBox(https://www.virtualbox.org/wiki/Downloads) installed, please install one of them.
	
	For either:
	Download the vmHTMAD.zip file from http://cs.calvin.edu/activities/htmad/
	Unzip the vmHTMAD.zip file
		This is done by:
		In Windows: Right-click on the vmHTMAD.zip folder and click on "extract all..." and follow the on-screen prompts
		On a Mac: Double-click on the vmHTMAD.zip folder, the archive manager will extract it
		In Linux: cd to where you have downloaded the vmHTMAD.zip file (probably your downloads folder, so "cd ~/Downloads") and run "unzip vmHTMAD.zip" (if t gives you an error, you probably need to install the "zip" and "unzip" utilities.
	
	In VirtualBox:
	Open VirtualBox
	Click File -> Import Appliance
	Click "Open Appliance"
	Navigate to where you downloaded the HTMAD VM (most likely in your Downloads folder)
	Go into the vmHTMAD folder and select the file vmHTMAD.ovf
	Click "Continue"
	Review the options and click "Import"
	It will now import the VM (This will take a while, we recommend a coffee break at this point in the instructions)
	Enjoy your VM!
	
	
	In VMWare Player:
	
	Click "Open Virtual Machine"
	Navigate to the vmHTMAD folder, and select the vmHTMAD.ovf file
	In the window that pops up, click "Import"
	It will now import the VM (This will take w while, we recommend a coffee break at this point in the instructions)
	Enjoy your VM!