Globus - core-unit-bioinformatics/knowledge-base GitHub Wiki

Globus

What is Globus?

Their own description and basic funding info:

"Globus is a non-profit service for secure, reliable research data management.
With Globus, subscribers can move, share, & discover data via a single
interface – whether your files live on a supercomputer, lab cluster,
tape archive, public cloud or your laptop, you can manage this data
from anywhere, using your existing identities, via just a web browser.
[...]
Globus is a group at the University of Chicago that develops and operates
a non-profit service for use by the research community.
[...]
Globus products and services are developed and operated by the
University of Chicago and Argonne National Laboratory,
supported by funding from the Department of Energy,
the National Science Foundation, and the National Institutes of Health​"

Problem: no folders but $HOME are accessible

By default, only the $HOME folder is readable/writable after setting up a new personal endpoint on a machine (say, your laptop). You can make additional folders accessible for Globus by editing this file:

$HOME/.globusonline/lta/config-paths

How to batch-download files on the command line?

This topic now has its own dedicated guide. ➡️ See the full guide here: Globus Downloads with enaBrowserTools

Common problem: finding the file path on Globus

EBI/ENA

File paths can be found in the file report of an accessioned entry, and look like this:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR323/000/ERR3239740/ERR3239740_1.fastq.gz

The same file can be located on the EBI/ENA Globus under this path:

/gridftp/ena/fastq/ERR323/000/ERR3239740/ERR3239740_1.fastq.gz

Note the simple change in the path prefix that distinguishes the FTP from the Globus location.

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