Making Galaxy wrappers dev environment setup

galaxy-wrappers-notes

# Rackspace Ubuntu 14.04
# 500 MB too slow
# Trying 1 GB General Purpose v1

ssh -L 8080:localhost:8080 root@${host}
su ubuntu

cd
sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get install git postgresql python-virtualenv
sudo apt-get build-dep xz-utils libtool python-biopython zlib1g libbz2-1.0 sqlite3 libgdbm3 trimmomatic
sudo su -s /bin/bash postgres -c 'cd; createuser -DRS ubuntu'
sudo su -s /bin/bash postgres -c 'cd; createdb -O ubuntu galaxy'

git clone https://github.com/galaxyproject/galaxy/
cd galaxy
git checkout master
virtualenv .venv
source .venv/bin/activate
pip install -U pip setuptools wheel
pip install khmer
cp config/galaxy.ini.sample config/galaxy.ini
mkdir -p tool_dependency_dir
sed -i 's/#admin_users = None/admin_users = crusoe@ucdavis.edu/' config/galaxy.ini
sed -i 's/#tool_dependency_dir = None/tool_dependency_dir = tool_dependency_dir/' config/galaxy.ini
echo 'database_connection = postgresql:///galaxy?host=/var/run/postgresql' >> config/galaxy.ini
#sh run.sh
# make user with email address 'crusoe@ucdavis.edu' at https://localhost:8080

cd ~
git clone git@github.com:mr-c/tools-iuc.git
cd tools-iuc
virtualenv env
source env/bin/activate
sudo apt-get install libxml2-utils
pip install -U pip setuptools planemo
git checkout khmer-wrappers
cd tools/khmer
planemo lint
# update wrapper
planemo shed_update --owner crusoe --shed_key ${shed_key} --shed_target toolshed 

GALAXY_TEST_DBURI=postgresql:///galaxy?host=/var/run/postgresql planemo test --galaxy_root /home/ubuntu/galaxy/