Due to a number of factors, the usegalaxy.org FTP service will be decommissioned on August 12, 2022. The service was first introduced in 2010 for uploading large data to Galaxy in a time when browser upload functionality was severely limited. Since that time, browser limitations on file sizes have been removed and protocols for reliable, resumable uploads have been developed and integrated into the Galaxy platform. Because of this, the need for the FTP service has greatly decreased. In addition, the proliferation of institutional firewalls and data security policies have blocked increasing numbers of people from even being able to access the FTP service.
One important use case served by the FTP service remains, however: uploading large data from remote systems (where one only has command-line access to data, not a web browser). Because moving data to a system with a web browser can be tedious and inefficient, we have developed a solution: The galaxy-upload command-line utility. This tool interacts directly with Galaxy’s web interface, meaning that it is firewall friendly. It supports resuming interrupted uploads and specifying upload parameters directly, so there is no need for the separate “import from FTP” step that is necessary when using the FTP service.
galaxy-upload is a Python package installable via pip:
$ pip install galaxy-upload
Once installed, you can upload from the command line to a Galaxy history like so:
$ galaxy-upload --url https://usegalaxy.org \ --api-key 70ffeec0ffeea11e1eaccede1337loaf --history-name 'Run 2' \ RUN2_F_001.fastq.gz RUN2_R_001.fastq.gz
Full usage details can be found in the documentation at https://galaxy-upload.readthedocs.org/