$ pip install ensembl-tui

$ uv sync

That creates a .venv/ with an editable install of the project plus all of the development dependencies. uv downloads a suitable Python itself, so you do not need one installed first. Run commands in that environment with uv run, for example

$ uv run eti --help

We use a plain text file to indicate the Ensembl domain, release and types of genomic data to download. Start by using the demo-config subcommand.

Usage: eti demo-config [OPTIONS]

  exports sample config and species table to the nominated path

Options:
  -o, --outpath PATH              Path to directory to export all rc contents.
  --domain [vertebrates|main|metazoa|protists]
                                  Ensembl domain to use for species list.
                                  [default: main]
  -f, --force_overwrite           Overwrite existing data.
  --help                          Show this message and exit.

$ eti demo-config -o ensembl_download

This command creates a ensembl_download download directory and writes two plain text files into it:

1. species.tsv: contains the Latin names, common names etc... of the species accessible at ensembl.org website.
2. sample.cfg: a sample configuration file that you can edit to specify the data you want to download.

The latter file includes comments on how to edit it in order to specify the genomic resources that you want.

Downloads the data indicated in the config file to a local directory.

Usage: eti download [OPTIONS]

  download data from Ensembl's ftp site

Options:
  -c, --configpath PATH    Path to config file specifying databases, (only
                           species or compara at present).
  -d, --debug              Maximum verbosity, and reduces number of downloads,
                           etc...
  -sm, --species_map TEXT  Tsv file with species names, abbreviations etc..
                           [default: main]
  -v, --verbose
  --help                   Show this message and exit.

For a config file named config.cfg, the download command would be:

$ cd to/directory/with/config.cfg
$ eti download -c config.cfg

Note This is the only step for which the internet is required. Downloads can be interrupted and resumed. The software will delete partially downloaded files.

The download creates a new .cfg file inside the download directory. This file is used by the install command.

Converts the downloaded data into data formats designed to enhance querying performance.

Usage: eti install [OPTIONS]

  create the local representations of the data

Options:
  -d, --download PATH       Path to local download directory containing a cfg
                            file.
  -np, --num_procs INTEGER  Number of procs to use.  [default: 1]
  -f, --force_overwrite     Overwrite existing data.
  -v, --verbose
  --help                    Show this message and exit.

This step can be run in parallel, but the memory requirements will scale with the number of genomes. So we suggest monitoring performance on your system by trying it out on a small number of CPUs to start with. The following command uses 2 CPUs and has been safe on systems with only 16GB of RAM for 10 primate genomes, including homology data and whole genome alignments.

$ cd to/directory/with/downloaded_data
$ eti install -d downloaded_data -np 2

Usage: eti installed [OPTIONS]

  show what is installed

Options:
  -i, --installed TEXT  Path to root directory of an installation.  [required]
  --help                Show this message and exit.

You can get help on individual subcommands by running eti <subcommand> in the terminal.

Usage: eti [OPTIONS] COMMAND [ARGS]...

  Tools for obtaining and interrogating subsets of https://ensembl.org genomic
  data.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  tui              Open Textual TUI.
  demo-config      exports sample config and species table to the nominated...
  download         download data from Ensembl's ftp site
  install          create the local representations of the data
  installed        show what is installed
  species-summary  genome summary data for a species
  dump-genes       export meta-data table for genes from one species to...
  compara-summary  summary data for compara
  homologs         exports CDS sequence data in fasta format for homology...
  alignments       export multiple alignments in fasta format for named genes