v3.2.0

What's New

• B-STILL backend — Added support for B-STILL (Bayesian Significance Test of Invariant Low Likelihoods), a modified FUBAR analysis that detects invariant sites. Includes analysis handler, shell execution script, server route, and router whitelist entry.

Dependency Updates

• Bumped socket.io from 4.1.2 to 4.6.2
• Bumped ajv from 6.12.6 to 6.14.0
• Bumped js-yaml from 3.14.1 to 3.14.2

v3.1.0 - Modernize PRIME Backend

What's Changed

• Modernized PRIME backend to use HyPhy CLI (PRIME.bf with --alignment, --tree, --code, --branches, --property-set, --pvalue, --impute-states) instead of the legacy stdin-piped batch file approach
• Added checkOnly validation mode, local/slurm/qsub execution support, and structured logging to prime.js
• Fixed PRIME route in server.js to merge tree data into job params (matching FEL, MEME, BUSTED, etc.)

v3.0.3

Bug Fixes

• GARD: Add ENV=TOLERATE_NUMERICAL_ERRORS=1; to HyPhy command line for all execution paths (#342)

v2.7.1

Bug Fixes

• GARD: Add ENV=TOLERATE_NUMERICAL_ERRORS=1; to HyPhy command line for all execution paths (#343)

v3.0.1

Bug Fixes

• GARD: Fix critical bug where datatype wasn't converted through the lookup table in the else branch. When self.params.datatype is "protein", it was passed directly to the shell script without converting to "amino-acid" (which HyPhy expects). (#341)

v3.0.2 - Non-MPI Execution

Changes

Bug Fixes

• Force all analysis methods to use HYPHYMP (non-MPI) exclusively to eliminate MPI library dependency issues
• Update MPI module loading to use lmod with gnu14 and openmpi5 for environments that support it

Technical Details

• Removed MPI dependency from 13 analysis scripts: absrel, bgm, busted, cfel, fade, fel, fubar, gard, meme, multihit, nrm, relax, slac
• Compute nodes don't have lmod, so MPI modules can't be loaded
• HYPHYMP provides better compatibility across all cluster environments

Improvements

• Simplified execution path reduces complexity and potential points of failure
• Better error handling and diagnostics
• Consistent behavior across all analysis types

Deployment

Production deployment on datamonkey3 server completed successfully.

3.0.0

3.0.0 Release

🔄 Unified Data Format

All analyses now accept a consistent data structure:

{
  alignment: "FASTA format data",
  tree: "Newick format data", 
  job: { /* analysis parameters */ }
}

📊 Updated Analyses

• FEL, MEME, SLAC, BUSTED, aBSREL, RELAX, GARD, FUBAR, FADE, Contrast-FEL, BGM, MultiHit, NRM

🏗️ Infrastructure Improvements

• job:status Socket.IO event for job reconnection
• Universal alignment data extraction
• Consistent tree data merging
• Shell scripts with intelligent HYPHY executable selection
• Multi-scheduler support (PBS/TORQUE, SLURM, local execution)

✅ Benefits

• Consistency across all analyses
• Easier client integration
• Better error handling and parameter validation
• Backward compatible with existing clients

v2.6.2 - Extended SLURM Support

What's Changed

SLURM Support Extended

• Added SLURM support to BGM, FADE, MULTIHIT, and NRM analysis methods
• Updated shell scripts for existing SLURM-enabled methods
• Added Slurm job queue tests with filtering for non-datamonkey jobs

Version

• Bumped version to 2.6.2

Full Changelog: 2.6.1...2.6.2

2.7.0

What's Changed

• Enhanced difFUBAR backend with robust NEXUS parsing and debugging by @stevenweaver in #329
• Add local execution support for bioinformatics analyses by @stevenweaver in #330

Full Changelog: 2.6.1...2.7.0

Release 2.6.1

Changes in 2.6.1

• Added slurm_partition parameter to config.json.tpl with 'datamonkey' as value
• Updated default partition fallback from 'defq' to 'datamonkey' in all job files
• Fixes SLURM partition configuration for all job types