How To Run borice
Download 13.53 Kb.
|
- Navigate this page:
- Instructions for Windows
- Instructions for Mac
- General Instructions
How To Run BORICE Before running, make sure the following files are placed on your desktop along with the data file called SSdata_borice.csv: BORICE.py, main.py, MyDoubleValidator.py, and BORICE_GUI.py. BORICE is written in Python. Go to the following website to download Python: http://www.python.org/download/ BORICE will work with either Python 2.7.2 or 3.2.2. We recommend installing 2.7.2 simply because, at the moment, more third party software is available for use with Python 2.7.2. If you do not plan to use Python for anything other than running BORICE, then it will make no difference which version you install. Make sure to download the installer that will work with your computer’s operating system. At the top of the BORICE code is the following: #!/usr/bin/env python This should tell your computer to link to the installed version of Python on your computer. It is possible you will need to specify the version by ending the line with the following: #!/usr/bin/env python2 or #!/usr/bin/env python3 But try using the default first. BORICE functions through a graphical user interface (GUI). In order for the GUI to function, you will need to install the following depending on your operating system: Instructions for Windows: You will need to install PyQt, which can be found at the following website: http://www.riverbankcomputing.co.uk/software/pyqt/download/ Download the installer (listed under “Binary Packages”) that is specific to the version of Python you have installed (2.7 or 3.2) and your operating system (Windows 32 or 64 bit). Instructions for Mac: The BORICE GUI was developed for use on Mac OS X Snow Leopard. It has not yet been tested on Lion. The following instructions assume that Snow Leopard is used. First, you must download the Xcode Developer Tools software. This is Xcode 3 for Snow Leopard. This can be found at the Mac Dev Center on the Apple website: https://developer.apple.com/devcenter/mac/index.action This is a free download, but you will likely need to register to obtain it. Once you have installed Xcode 3, you will then need to download the Qt SDK at the following website: http://qt.nokia.com/downloads/sdk-mac-os-cpp Once you have installed Qt SDK, you will need to install SIP and compile it from the source code. Download SIP from the following website: http://www.riverbankcomputing.co.uk/software/sip/download Make sure to choose the package that is compatible with Mac OS X. To compile SIP from source, you will need to do the following: Open the terminal window by going to Macintosh HD => Applications => Terminal. Then change your working directory to the SIP folder by typing: cd /Users/ your_user_directory_name/sip-4.12.4 Then type: python configure.py Once that is finished, type: make When that is completed, type: make install That will finish the SIP installation. Now you need to install PyQt from the following website: http://www.riverbankcomputing.co.uk/software/pyqt/download Again, this must be compiled from source, and you need to download the source code for Mac OS X. To install PyQt, reopen the terminal window. Then change your directory to the following: cd /Users/ your_user_directory_name/PyQt_4.8.5 Then type: python configure.py Once that is finished, type: make When that is completed, type: make install Once you have successfully installed PyQt, reopen the terminal window. Then change your working directory to your desktop by entering the following at the command line and hit enter: cd /Users/your_user_directory_name_goes_here/Desktop General Instructions: Once you have successfully changed your working directory to your desktop, make sure that all of the necessary BORICE files (main.py, MyDoubleValidator.py, BORICE_GUIv1.py, and BORICEv17.py) and your input data file are on the desktop. On a Mac, enter the following at the command line and hit enter to execute the GUI: python main.py On a PC, double-click on main.py to execute the GUI. From the file menu, select “Open Data File”. Then select your input data file. You will then have the option to run BORICE with default settings or to change the settings. The following defaults are listed under the “General Settings” tab: Number of Steps = 100000 Number of Burn In Steps = 9999 Outcrossing Rate Tuning Parameter = 0.05 Allele Frequency Tuning Parameter = 0.1 Initial Population Outcrossing Rate = 0.5 The number of steps is the number of steps taken in the MCMC chain. The number of burn in steps is the number of initial steps that will be discarded before the posterior distributions are calculated. The outcrossing rate tuning parameter is the value that determines how large a change in outcrossing rate is made at each step. The allele frequency tuning parameter is the value that determines how large a change in allele frequency is made at each step. The initial population outcrossing rate is the starting outcrossing rate value for the chain. You also have the option of choosing the output files from your BORICE run under the “File Output Options” tab. The default settings are to produce all files. Output 1 is always produced; it contains the posterior distributions of t and F, population inbreeding history, and allele frequencies at each locus. Output 2 contains the posterior distributions of maternal inbreeding histories. Output 3 contains the list of t and F values from every 10 steps in the MCMC chain. Output 4 contains the posterior distributions for each maternal genotype at each locus in each family. The “Input Data Summary” tab shows you the number of marker loci, number of families, and number of individuals read from your input data file. If these numbers are not correct, then you should check your input datafile. The “Locus Settings” tab allows you to choose whether to run each locus as having null alleles or not. The default setting is all boxes unchecked, which means null alleles will not be considered at a locus. Checking a locus box means null alleles will be considered at that locus. Click “Run” to run BORICE. Any errors that occur during the run will appear in the Command Prompt or Terminal window. Directory: hdy -> journal journal -> Priors used for approximate bayesian computation (abc) analyses. N1= Effective population size journal -> Statement of Download 13.53 Kb. Share with your friends:
|