DNAWorks

1-5 minutesPaperCodeProduction Ready

Automatic oligonucleotide design for PCR-based gene synthesis

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: compiled/binary SIF or shared python312_slim + ext3 overlay
Next: Production Ready. Optional hardening: expose more DNAWorks synthesis parameters and add nucleotide-input benchmark coverage.

DNAWorks source staged from davidhoover/DNAWorks rev f8536579af1c39372687917e3f0b61de3cf04676; binary reports DNAWorks 3.2.4. Built with gfortran 13.3.0/GNU Make 4.3; target size ~34 MB; license GPL-2. Slurm job 406 ran bundled sample successfully with exit 0, empty stderr, 300 nt/100 residues/2 oligos final summary. Local Bio Mega runner adapter added 2026-07-02 for bounded protein/nucleotide inputs, using shared CPU SIF strategy and staged DNAWorks binary paths; fresh backend recheck was blocked by SSH/Tailscale timeouts from this workstation. 2026-07-05 production evidence: patched runner adapter to pass local dnaworks.inp filename from the output working directory, avoiding DNAWorks path parsing truncation. Runner API remote id b95f9b4279b1 submitted Slurm job 426. Job completed with artifact manifest containing dnaworks.inp, dnaworks.log, dnaworks.stdout, dnaworks.stderr, job.log, results.csv, summary.json, slurm.out, and slurm.err. Protein input length 29 generated 87 nt coding sequence and 4 oligonucleotides in DNAWorks log/stdout; stderr and slurm.err were empty. GPL-2 source/license noted from staged upstream.