European Nucleotide Archive (ENA)
A simple CLI toolbox to use theena-utils is a small python package that provides a CLI to submit nucleotides sequences to the European Nucleotide Archive (ENA).
The goals of this package are:
- To facilitate the submission of large numbers of objects
- To ease the exploitation of the ENA metadata schema to its full potential (see the Future developments section below)
This is an early development version that provides only minimal features.
Supported submission types
- Non-multiplexed paired-end sequencing reads
Features
- File upload
- Study registration
- Experiment registration
- Run registration
- Sample registration
Requirements
- Python3
- Webin account
Installation
The latest release is available on PyPI and can be installed using pip
:
$ pip install ena-utils
pipx
Isolated environments using Install and execute ena-utils in an isolated environment using pipx
.
Install pipx
and make sure that the $PATH
is correctly configured.
$ python3 -m pip install --user pipx $ pipx ensurepath
Once pipx
is installed use following command to install ena-utils
.
$ pipx install ena-utils $ which ena-utils ~/.local/bin/ena-utils
Usage
The latest documentation is available at https://readthedocs.org.
Future developments
- Auto-generation of the CLI and objects lists templates from the ENA schema XSD files.