enaBrowserTools provides the most straightforward way to retrieve sequencing data from EBI/ENA: instead of constructing Globus paths, preparing file lists, or managing batch transfers, you supply a project, study, sample, or run accession, and the tool automatically downloads all associated files. This makes it the preferred method for ENA data retrieval on Hilbert and removes nearly all manual steps required in the traditional Globus-based workflow.

This guide describes how to retrieve sequencing data for project PRJEB58625 on the Hilbert HPC system using Globus and the ENABrowserTools.

ssh [email protected]

Once logged in, move to a storage node:

ssh hpc-storage-14k-1

(Alternatively, you may connect to hpc-storage-14k-2 if preferred.)

On the storage node, load the Globus environment and log in:

module load Globus
globus login --no-local-server

You’ll be prompted to follow the login steps in your browser (follow the instructions):

⚠️ The storage nodes do not allow direct Git cloning. You must clone the repository locally, then transfer it to your Hilbert directory.

Clone the ENA Browser Tools on your local machine:

git clone https://github.com/enasequence/enaBrowserTools.git

Transfer the cloned folder to your Hilbert storage directory.

Once the repository is available on Hilbert, navigate to the Python3 directory:

cd enaBrowserTools/python3/

Execute the download command for PRJEB58625:

./enaGroupGet -g read -f fastq -d /path/to/target_directory/ PRJEB58625

This command will download all project-related FASTQ files into your specified directory.

For a detailed explanation of available parameters and usage examples, visit the official ENA Browser Tools documentation:

👉 ENA Browser Tools on GitHub