vagrant_instructions

Install vagrant via vagrantup.com. Vagrant enables the quick, easy 
installation of customizeable virtual machines. The default is a 32-bit Ubuntu
12.04 box. It works really cleanly for developing these machines. I'm 
currently figuring out how to share my personal machine (without having to
pay for it). 

##To start Vagrant:
vagrant init hashicorp/precise32
vagrant up
vagrant ssh

##To set up treePL:

sudo apt-get install git
sudo apt-get install make
sudo apt-get install libtool
sudo apt-get install autoconf
git clone git://github.com/blackrim/treePL.git
cd treePL/
cd deps/
tar xvf adol-c_git_saved.tar.gz 
tar xvf nlopt-2.2.4.tar.gz 
rm *.gz
cd nlopt-2.2.4/
./configure 
make
sudo make install
cd ../adol-c
autoreconf -fi
sudo ./configure --with-openmp-flag=-fopenmp --prefix=/usr
make
sudo make install
cd ../src	
./configure
sudo make install

##To copy files to Vagrant box:

scp -P 2222 <file> vagrant@localhost:.

Password is 'vagrant'

##Once all your files are in Vagrant

treePL doesn't play well with Mac/Windows line endings. So, we shall switch them to *nix line endings

for file in *.txt; do sed -i 's/\r/\n/g' $file; done

Alter as needed to change all your files to *nix line endings.

treePL also gets weird about rooting. If you've rerooted your tree in a software that leaves a [&R] tag, this might cause a segmentation fault ... for some reason.

sed -i 's/\[&R]//g' your_file

should fix this.

###To run treePL

Place your config file and your tree (if in a separate file) into the treePL directory. Call as such:

./treePL treePLmatt

To call in a loop for multiple trees:

for file in *.tre ; do cp $file input.txt; ./treePL config ; cp dated.tre $file.tre; done

In your config file, set treefile = input.txt