galaxy-fsspec

An fsspec filesystem that exposes a Galaxy account as a virtual, read-only directory tree.

galaxy://
├── histories/
│   └── <history>/                 (created / last_modified exposed via info())
│       ├── <dataset>              (files)
│       └── <collection>/          (list, paired, list:paired, nested ...)
│           └── ...                (collections nest as folders of folders)
└── libraries/
    └── <library>/
        ├── <dataset>
        └── <folder>/
            └── ...

Datasets are streamed as files; collections (including nested collections) appear as directories.

Install

uv pip install galaxy-fsspec

Because the protocol is registered via the fsspec.specs entry point, fsspec.filesystem("galaxy") and fsspec.open("galaxy://...") work without any extra imports.

Configure

The filesystem reads two environment variables:

Optional:

You can also pass arguments explicitly:

import fsspec
fs = fsspec.filesystem("galaxy", url="https://my.galaxy.org", api_key="...", show_hid_in_names=True)

Usage

import fsspec

fs = fsspec.filesystem("galaxy")

# List histories.
for h in fs.ls("histories", detail=True):
    print(h["name"])

# Timestamps (created / last_modified) are fetched lazily via info().
for h in fs.ls("histories", detail=True):
    info = fs.info(h["name"])
    print(info["name"], info["created"], info["last_modified"])

# Walk a history's contents — datasets are files, collections are folders.
print(fs.ls("histories/My History"))

# Read a dataset (range-aware streaming via Galaxy's display endpoint).
with fs.open("histories/My History/my-paired/forward/R1.fastq", "rb") as f:
    print(f.read(64))

show_hid_in_names=True renders history entries as Galaxy does in its UI:

histories/My History/1-my-uploaded-dataset
histories/My History/30-my result
histories/My History/5-mycollection/1-forward

Scope

Read-only for now: histories, datasets, and (nested) collections. Writes, uploads, and library browsing are not yet supported.