A simple CLI toolbox to use the European Nucleotide Archive (ENA)
ena-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.
- Non-multiplexed paired-end sequencing reads
- File upload
- Study registration
- Experiment registration
- Run registration
- Sample registration
- Python3
- Webin account
The latest release is available on PyPI and can be installed using pip
:
$ pip install ena-utils
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
The latest documentation is available at https://readthedocs.org.
- Auto-generation of the CLI and objects lists templates from the ENA schema XSD files.