BaseSpace Run Uploader

Author: Fadi Slimi
© 2025 Fadi Slimi – Medibio (Official Partner Illumina – North Africa)

A friendly and automated Bash pipeline to upload NGS Run folders to Illumina BaseSpace, including authentication, checksum verification, and log generation. Designed for Linux systems for reproducible and client-friendly use.

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Overview

This Bash script simplifies the upload of sequencing runs (Illumina MiSeq, NextSeq, NovaSeq, etc.) to BaseSpace. It automates the following steps:

• Checks for the BaseSpace CLI (bs) and installs it if missing.
• Performs user authentication via BaseSpace CLI.
• Optionally standardizes FASTQ file names.
• Generates MD5 checksums for all files in the RUN folder.
• Uploads the run to BaseSpace with a single command.
• Provides clear color-coded terminal output and log files for easy tracking.

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Features

• Automatic BaseSpace CLI installation if missing.
• User authentication handling directly from the script.
• Optional FASTQ standardization for Illumina naming conventions.
• Instrument detection (MiSeq, NextSeq, NovaSeq, etc.).
• MD5 checksum generation for data integrity.
• Retry + Resume upload in case of network failure.
• Color-coded output for clarity (info, warnings, errors).
• Log file generation for each upload session.

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Requirements

• Linux-based OS (tested on Ubuntu 20.04+).
• Bash shell (v4+).
• Internet connection for BaseSpace CLI installation and authentication.
• Illumina BaseSpace account.

Note: Windows users will need to adapt the script to PowerShell.

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Installation

Clone the repository:

git clone https://github.com/your-username/BaseSpace_RunUploader.git
cd BaseSpace_RunUploader
chmod +x BaseSpace_RunUploader_v3.3.sh

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Usage

Run the script:

./BaseSpace_RunUploader_v3.3.sh

You will be prompted for:

1- Full path to the RUN folder (e.g., ~/Runs/Run_2025-11-17)

2- Name of the run (default: folder name)

3- Instrument type (MiSeq, NextSeq, NovaSeq, etc.)

4- Option to standardize FASTQ files (yes/no)

After confirmation, the script will:

• Authenticate with BaseSpace CLI (if needed).

• Generate md5sum.txt for all files in the run folder.

• Standardize FASTQ files (if chosen).

• Upload the run to BaseSpace.

• Save a log file in ./logs/ with all actions.

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Logging

All actions and messages are logged in: ./logs/upload_YYYYMMDD_HHMM.log for auditing and troubleshooting purposes.

License

This project is licensed under the MIT License – see LICENSE.txt for details. © 2025 Fadi Slimi – Medibio (Official Partner Illumina – North Africa)

Contributing

Contributions are welcome! Please submit bug reports, feature requests, or pull requests via GitHub.

Example

./BaseSpace_RunUploader_v3.3.sh
Enter path: ~/Runs/Run_2025-11-17
Enter run name: My_Run
Enter instrument: NextSeq2000
Standardize FASTQ files? yes

Included Files

• BaseSpace_RunUploader_v3.3.sh — Main Bash pipeline script

• LICENSE.txt — License file

• CHANGELOG.txt — Version history

• README.md — This file

• logs/ — Directory for automatically generated logs (created by the script)

• modules/ — Optional modules (if any)

Notes

• Designed for client-friendly use, reproducibility, and traceability.

• Fully supports Linux environments.

• Easy to customize and extend for future sequencing instruments or workflow needs.