Installation

Dependencies

Python 3.3 or greater with the following packages installed:

1. awscli
2. google-api-python-client
3. inflection
4. jsonschema
5. requests
6. urllib3

Installation

pip3

Central installation

pip3 install encode-utils

User installation

pip3 install --user encode-utils

The latter way is useful if you are worried about overwriting any scripts that other packages already installed in your Python installation - You knew that pip would do this, without warning you, right?

virtualenv with pip3

Make sure to have the virtualenv Python package already installed, and then run the following commands (where eu is the name of the output directory to contain the virtual environment):

virtualenv eu
source eu/bin/activate
pip3 install encode-utils

This is the most secure of the outlined methods for isolating your Python environment for use with this package (and any given package for that matter).

Upgrade

pip3 install -U encode-utils

Installing the master branch

pip3 install https://github.com/StanfordBioinformatics/encode_utils/archive/master.zip

Manual Install

1. Create a folder called encode_utils in a location where you will store releases of this tool.
2. Download the latest release (or clone master) into this new folder, and unpack the tarball or zip file. For example, if the release is tagged as 1.0.0, you should now have the folder path /prefix-path/encode_utils-1.0.0, where prefix-path is folder path you chose to contain the release.

Setup

You'll need to update your PATH and PYTHONPATH environment variables. First, create the following variable to make the following steps easier:

EU_RELEASE=/prefix-path/encode_utils-1.0.0

1. Update your PYTHONPATH environment variable as follows:

   export PYTHONPATH=${EU_RELEASE}:${PYTHONPATH}
   

2. Update your PATH environment variable as follows:

   export PATH=${EU_RELEASE}/encode_utils/MetaDataRegistration:${PATH}
   export PATH=${EU_RELEASE}/encode_utils/scripts:${PATH}
   

If you use environment modules on your system, you could wrap these commands in such a module.

Configuration

See the configuration wiki page.