BiocHubsIngestR

R package for uploading data to Bioconductor Hubs Ingest endpoints.

Description

BiocHubsIngestR provides tools for uploading data to temporary S3 endpoints created by the Bioconductor Hubs Ingest stack. It uses the paws SDK for R to handle S3 operations and provides a simple interface for authentication and file uploads.

Prerequisites

Before using this package, you must:

1. Have an S3 ingestion endpoint generated by a Bioconductor admin
2. Receive access credentials (username and password) from the admin

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Bioconductor/BiocHubsIngestR")

Usage

Authentication

# Set up credentials (provided by Bioconductor admin)
BiocHubsIngestR::auth(username = "your_username", password = "your_password")

Uploading Data

# Upload a single file
BiocHubsIngestR::upload("path/to/your/file.txt")

# Upload an entire directory
BiocHubsIngestR::upload("path/to/your/data/directory")

Important Notes

1. After completing your data upload, notify the Bioconductor admin you are coordinating with
2. Once you inform the admin that the upload is complete, the endpoint will be locked for processing
3. No further uploads will be possible after the endpoint is locked

Support

For questions or issues:

• Open an issue on the GitHub repository
• Contact the Bioconductor team