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

After this step, a bare pops call anywhere on the command line should work and return the help output. In case pops is not executable on the command line, the POPScomp app you will not work, instead it 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

If those warnings appear, please go back to the previous step and make sure the pops binary is working and in a binary path that is recognised by the operating system ($PATH).

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>)