Installation

In order to install angsd-wrapper fully, you need to follow a few steps:

First, you need to make the ANGSD executable and the associated programs:

1. $ git clone https://github.com/arundurvasula/angsd-wrapper.git
2. $ cd angsd-wrapper/angsd
3. $ make
4. $ cd ../ngsPopGen
5. $ make
6. $ cd ../ngsF
7. $ make

Note: some people receive the following error when compiling:

g++ -O3 -D_USE_KNETFILE  -o angsd.static *.o -lz -lpthread --static                                             
/usr/bin/ld: cannot find -lz                                                                                    
collect2: ld returned 1 exit status                                                                             
make: *** [angsd.static] Error 1  

This is an error related to zlib and can be corrected by contacting your system administrator. See here for example: http://stackoverflow.com/questions/3373995/usr-bin-ld-cannot-find-lz or here: http://askubuntu.com/questions/377000/compilation-error-usr-bin-ld-cannot-find-lz

Then you need to install the requisite R packages for using the R graphing application:

1. $ R
2. > install.packages("shiny")
3. > install.packages("ape")
4. > install.packages("Hmisc")
5. > install.packages("lattice")
6. > source("http://bioconductor.org/biocLite.R")
7. > biocLite("genomeIntervals")
8. > install.packages("data.table")