Friday, July 31, 2015

PICS-Ord on Mac

In a previous post, I wrote about how to get the program PICS-Ord to run easily on a PC. Other operating systems presented some special problems associated with getting the different dependencies to find one another. I recently found Homebrew, which solves a lot of the problems typically found with Mac computers, and I put together some instructions for running PICS-Ord on the current Mac OS.

Running PICS-Ord on Mac OS X (10.9 or 10.10):

(1) Download and install R from here:
https://cran.r-project.org/bin/macosx/R-3.2.2.pkg
Open the file and follow the instructions.

(2) Install CMake and Boost using Homebrew; use the following three commands in the terminal to first install Homebrew and then the two Ngila dependencies:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install cmake
brew install boost --with-python


(3) Install Ngila by using the following commands in the terminal (if you already have wget, you can ignore the first line):
brew install wget
wget http://scit.us/projects/files/ngila/Releases/ngila-release.tar.gz
tar zxvf ngila-release.tar.gz
cd ngila-1.3-release/
cmake . && make
make install
cd ..


(4) Download PICS-Ord from here:
http://scit.us/projects/files/ngila/picsord.zip
Open the zip file to create the picsord directory.

(5) Run PICS-Ord by moving the FASTA files into the picsord directory, navigating to the picsord directory in the terminal, and running the following:
Rscript picsord.R region_1.fas > region_1.phy
Rscript picsord.R region_2.fas > region_2.phy
Rscript picsord.R region_3.fas > region_3.phy
Rscript picsord.R region_4.fas > region_4.phy


- Brendan

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Reference

L├╝cking, R., B. P. Hodkinson, A. Stamatakis, and R. A. Cartwright. 2011. PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinformatics 12: 10.
Download publication (PDF file)
Download R-based program (zipped program package)
View program wiki (website)

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