Download and install bpp (v.3.3) locally (into ~/local/src/bpp/src)

install_bpp.sh

## save our current directory so we can come back here when we're done
WORKDIR=$(pwd)

## To install local software I keep a directory in my home dir called 'local/'
## the command below will make this dir if it does not already exist.
mkdir -p ~/local/src/

## move into your local/src directory 
cd ~/local/src

## download the file here, since this is where you store source code
curl -LkO http://abacus.gene.ucl.ac.uk/software/bpp3.3.tgz 2>/dev/null

## unpack the archive file and remove the download file
tar -xf bpp3.3.tgz
rm bpp3.3.tgz

## cd into the new bpp directory, and into its src/ directory
cd bpp3.3/src

## compile to create a binary executable called 'bpp'
## if you are on a HPC cluster you _may_ need to load the gcc compiler. 
## if you want to suppress the warnings add '2>/dev/null` to the end.
gcc -o bpp -O3 bpp.c tools.c -lm  2>/dev/null

## print the location of your bpp binary and success of installation
success=$(2>&1 ./bpp ../)
if [[ $success == *"bp&p"* ]]
then
  (>&2 echo "Hoorah, bp&p was successfully installed here: $(pwd)/bpp")
  (>&2 echo "Be sure to call it by entering the full path to the binary above.")
  ## copy the binary to local bins
  cp ./bpp ~/local/bin/
else
  (>&2 echo "installation failed -- uncomment '2>/dev/null' to see errors. ")
fi

## cd back home, even though jupyter would do this anyways
cd $WORKDIR