Front end, browser-based GUI for the IMa suite of evolutionary biology analysis tools. This repository contains code for linux/mac/windows versions (mac version is currently untested but will be shortly)

##Required Software

• node.js
• A web browser

To install node.js, use one of the following methods: ####Linux (apt-get) Run the following command in a terminal:

sudo apt-get install nodejs

To test the installation, run:

node -v

If this returns "command not found", run the command:

nodejs -v

If this runs, a symbolic link must be created to run node.js properly. Enter the following command:

sudo ln -s /usr/bin/nodejs /usr/bin/node

Otherwise, try using apt-get to download a different version of node.js:

sudo apt-get install nodejs-legacy

####Linux (yum) Run the following command in a terminal:

sudo yum install nodejs npm

You can test for a successful install by running "node -v" as shown above.

Additional linux installation methods can be found here

The node.js installer can downloaded here. Alternatively, it can be installed using brew:

brew install node

The windows installer can be found here

##Installation

1. Clone via commandline or download and unzip archive from this page.

• To clone, make a new directory and run this command in the target install directory:

git clone git://github.com/jaredgk/IMgui

• If downloading archive, open a terminal and navigate to your target directory:

cd /path/to/target/dir/

2. In a terminal, run the following command:

npm install

##Run

1. To start the node.js application, run the following command:

node index.js

2. Open a web browser window, and type the following path in the address bar:

localhost:3000

Note that closing this terminal or killing the node.js process will end all active IMa2 jobs started by the front end. However, closing the browser window will not affect any running jobs. ##Features The IMgui front end had three pages: the Job Manager, Output/Burntrend Analysis, and IMfig Generation.

###Job Manager The job manager will allow users to provide input file paths, an output file tag, a run mode (MCMC or load-genealogy), and other command line parameters. The browser will verify that selected parameters are compatible, and an option is provided to verify that the input files provided are present on the local filesystem. (Note that it will not validate the contents of the files)

Once a job is started, it will be added to the drop-down list above the text output box on the bottom of the page. From here, users can select a job to view output tables that are being generated, and control the state of the job by stopping/restarting/deleting an active job. User defined control of the run via IMrun/IMburn files can also be controlled from this area.

###Output/Burntrend Analysis The analysis page provides an XML parser to view tables and histograms contained in the output XML files from a run. To view, select a file and click the Analyze button.

If the file provided is a table file, ([out-prefix].xml or [out-prefix].intervals.xml) the first table will be auto-generated and displayed, with the drop-down menu that appears containing all of the tables provided in the file. These tables can be saved with the Save as .csv or Save as .png buttons. An optional filename can be provided in the text box above the save buttons.

If the file provided is a histogram file, ([out-prefix].histograms.xml) two drop-down menus will appear. The top one lists histogram sets provided in the file, the bottom will provide variables that can be graphed. Once Make Graph is clicked, a graph will be generated. Below the graph is the Code section, which can create a basic plotting script of the graphed variable in MATLAB, maplotlib, or R. A maximum line length can be provided if the script will be copied into an IDE with a line limit. Clicking the Generate Code button will then generate code, which can either be copied into a new file or downloaded with the Download Code button. (An filename prefix can be provided in the marked textbox)

###IMfig The IMfig page is a GUI for the IMfig plotting script, which displays population size, migration rates, and split time parameters with confidence intervals. The only required field in the input file name, all other parameters are optional, mostly to control formatting and color of the output file. Clicking the Submit button will pass the parameters to the IMfig executable included with the distribution. If the run is successful, a .jpg image of the resulting .eps file will display in the browser. From here, the image can be downloaded by right clicking and selecting Save Image As.... The image and the .eps file can also be accessed from the public/ folder in the IMgui directory.

Additional information is available on the help page which can be accessed via the link menu on the left of the page.