Installation

POPScomp Source Code

Download the latest POPScomp release.

https://github.com/Fraternalilab/POPScomp/releases/latest

Assuming the latest version is x.y.z, download the tar.gz file and unpack it.

wget https://github.com/Fraternalilab/POPScomp/archive/vx.y.z.tar.gz
tar -zxvf POPScomp-x.y.z.tar.gz
cd POPScomp-x.y.z

Alternatively, clone the GitHub repository, accepting the caveats of a development version.

git clone https://github.com/Fraternalilab/POPScomp

POPSC

Compile the POPSC pogram, which will be in src/pops.

cd POPSC
./bootstrap
./configure
make

Install the pops program (with root or sudo privileges)

make install

or create a symbolic link to it.

ln -s <path_to_POPScomp>/POPSC/src/pops /usr/local/bin/pops

Adjust the path to the 'pops' binary in POPSR/inst/popsr/app.R and POPSR/R/popscomp.R . The default setting is:

pops_shiny = c("/build/install/usr/local/bin/pops")

and that should be changed to

pops_shiny = c("/usr/local/bin/pops")

An unsuccessful call of the pops binary will create the following type of warnings:

Warning in system(command) : error in running command
tail: cannot open '/tmp/POPScomp_b0238b38976d6ab207c98c364f5918bb/*.iso.rpopsAtom' for reading: No such file or directory

POPSR

You need to have the XML and Z libraries installed on your operating system, both the base package and the development package. In the POPScomp root directory:

R CMD build POPSR
R CMD INSTALL POPSR

This step installs the popscomp.R function and others as loadable library POPSR.

Shiny App

You may run the Shiny app from RStudio. Open the file POPScomp/POPSR/inst/popsr/app.R in RStudio and press button Run App. That launches the Shiny interface and you are ready to pops. In case library packages are missing (all required libraries are listed at the top of app.R) install them via

install.packages(<package_name>)

The POPSR package can be installed from GitHub:

install.packages("devtools")
devtools::install_github("https://github.com/Fraternalilab/POPScomp")