Changelog

All notable changes to the RNA-seq Bioinformatics Toolkit Docker image will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.1] - 2025-07-09

ggridges R package: Added to CRAN package installation for enhanced ridge line plotting capabilities
Man pages support: Added man-db package and ran unminimize to restore documentation
Educational Linux commands: Users can now use ‘man’ command to learn basic Linux commands within the container

Column command package: Replaced util-linux with bsdextrautils for better column command functionality
Docker group setup: Simplified by removing macOS-specific staff group configuration
Course documentation: Updated various course posts with improved instructions for Docker approach

Column command functionality: Fixed missing bsdextrautils package for proper column command support

Apache Web Server: Configured to serve /workspace directory on port 8080
vim text editor: Added for command-line file editing
bedtools 2.31.1: Genomic arithmetic operations tool
Docker CLI tools: For running other bioinformatics containers
less command: Added to runtime dependencies for better terminal experience
util-linux package: Provides ‘column’ command and other utilities
RNA-seq course environment variables: Comprehensive set added to bashrc
Automatic Docker socket permission fixing: Cross-platform compatibility
start-services.sh script: Streamlined container initialization
Docker socket troubleshooting documentation: Comprehensive examples and guides

BREAKING: Switched from Docker-in-Docker to host Docker engine approach for better stability
Docker startup process: Improved with ENTRYPOINT + CMD pattern for proper signal handling
Apache configuration: Enhanced with ServerName directive and workspace symlink
README organization: Streamlined by merging redundant sections
Docker run examples: Updated to include port mapping (-p 8080:8080)
FastQC installation: Fixed to include complete directory structure and JAR files
PATH environment: Updated to include FastQC directory for proper execution

Interactive session stability: Eliminated glitchy sessions caused by Docker-in-Docker setup
Docker socket permissions: Automatic fixing on macOS and Linux systems
Apache configuration: Fixed workspace directory permissions
Container startup reliability: Improved performance and stability
FastQC execution: Fixed installation to ensure proper tool functionality

Added ncurses development libraries (libncurses5-dev, libncursesw5-dev) to runtime dependencies
Fixed missing “&&” operator in runtime apt-get install command

Enhanced container usability by allowing users to compile ncurses-dependent tools like samtools inside the running container

Initial release of the RNA-seq Bioinformatics Toolkit
Ubuntu 22.04 LTS base image with x86_64 architecture
Multi-stage build optimization for reduced image size
Comprehensive bioinformatics tools suite including:
- SAMtools, bam-readcount, HISAT2, StringTie, gffcompare
- htseq-count, TopHat, kallisto, FastQC, MultiQC
- Picard, Flexbar, Regtools, RSeQC, bedops
- gtfToGenePred, genePredToBed, how_are_we_stranded_here
Python 3 environment with scientific computing packages
R 4.x with essential bioinformatics libraries
Bioconductor packages for RNA-seq analysis