overwrites your ~/.opentree and builds a tree in ~/OpenTree/

synth-tree-from-scratch.sh

#!/bin/bash

cd ~
mkdir OpenTree
cd OpenTree/
git clone https://github.com/mtholder/propinquity.git

echo '[opentree]' > ~/.opentree
echo "home = $PWD" >> ~/.opentree
echo 'peyotl = %(home)s/peyotl' >> ~/.opentree
echo 'ott = %(home)s/ott/ott2.10draft11/' >> ~/.opentree
echo 'phylesystem = %(home)s/phylesystem' >> ~/.opentree
echo 'collections = %(home)s/phylesystem' >> ~/.opentree

mkdir ott
cd ott
wget http://files.opentreeoflife.org/ott/ott2.10/ott2.10draft11.tgz 
tar xfvz ott2.10draft11.tgz
mv ott ott2.10draft11
cd ..

git clone https://github.com/mtholder/peyotl.git
virtualenv env
source env/bin/activate
cd peyotl/
pip install -r requirements.txt 
python setup.py develop
python setup.py test
cd ..

mkdir -p phylesystem/shards
cd phylesystem/shards
git clone https://github.com/OpenTreeOfLife/phylesystem-1.git
git clone https://github.com/OpenTreeOfLife/collections-1.git
cd ../..

git clone https://github.com/mtholder/otcetera.git
cd otcetera/
sh bootstrap.sh 
mkdir buildgcc
cd buildgcc
bash ../reconf-gcc.sh 
make -j8 
make check
make install
cd ./installed/bin
export PATH="${PATH}:${PWD}"
cd ../lib/otcetera
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PWD}"

cd ~/OpenTree/propinquity/
pip install Chameleon
bash test.sh
bash bin/build_at_dir.sh config.opentree.synth ../test-opentree