Installation

Dependencies

Python 3.3 or greater with the following packages installed:

1. awscli
2. json
3. requests
4. urllib3

Installation

You can use pip3, do a manual install, or use VirtualEnv + pip. I'll discuss the first two methods below. If you read on up VirtualEnv, you'll know how to install this package with pip in a virtual environment.

pip3

Central installation

pip3 install https://github.com/StanfordBioinformatics/encode_utils/releases/latest

User installation

pip3 install --user https://github.com/StanfordBioinformatics/encode_utils/releases/latest

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

See the virtualenv docs for how to setup your virtual environment (very simple), then use pip3 as described above.

Upgrade

pip3 install -U https://github.com/StanfordBioinformatics/encode_utils/releases/latest

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 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.