Installation from git:

Note

It is strongly advised to use virtualenv to install the module locally.

git clone https://bitbucket.org/ffavero/bio_pype
cd bio_pype
python setup.py test
python setup.py install

Using virtualenv:

This code guide thought the installation and use of virtualenv when the main python installation does not include the virtualenv module.

mkdir ~/venv_files
# Download virtualenv files (not installed in the python version
# used in computerome)
curl -L -o ~/venv_files/setuptools-20.2.2-py2.py3-none-any.whl \
   https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/setuptools-20.2.2-py2.py3-none-any.whl
curl -L -o ~/venv_files/pip-8.1.0-py2.py3-none-any.whl \
   https://github.com/pypa/virtualenv/raw/develop/virtualenv_support/pip-8.1.0-py2.py3-none-any.whl
curl -L -o ~/venv_files/virtualenv.py \
   https://github.com/pypa/virtualenv/raw/develop/virtualenv.py

# Create a virtual environment
python ~/venv_files/virtualenv.py --extra-search-dir=~/venv_files \
   ~/venv_bio_pype
# Activate the environment
source ~/venv_bio_pype/bin/activate

# Install bio_pype as instructed above from git

# The pype command line utility will be available upon the "activation"
# of the environment or by specifying the full path, in this case:

# ~/venv_bio_pype/bin/pype

# To deactivate the virtual env:
deactivate