Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_validated_runner_api_slurm_orthrus
- Storage
- <5GB
- Strategy
- shared python312_slim.sif + tool ext3 overlay
- Next
- Production Ready. Optional hardening: expose user-uploaded screen/batch TSV inputs in the UI, preserve the CHyMErA vignette regression payload, and add a compact API regression test for condition plus combinatorial scoring.
SOP agent installed Orthrus R package HenryWard/orthrus revision 595703e771ccfded0825e9fc0fa7290bf66d1050 version 0.4.4.0 at /media/nik/seagate_nik/bio_server/repos/tools/orthrus with wrapper /media/nik/seagate_nik/bio_server/tools/orthrus/bin/orthrus-runner and R lib /media/nik/seagate_nik/bio_server/envs/tools/orthrus/Rlib. Native smoke benchmark failed after 37.42s, max RSS 292240 KB, in score_conditions_vs_control with invalid times argument on packaged CHyMErA vignette data. Log: /media/nik/seagate_nik/bio_server/logs/orthrus/native_20260701_230411.log. No Slurm job submitted because native runner failed first. 2026-07-09T15:29:20+08:00 SOP recheck: backend wrapper path was corrected from old external-drive mount to /media/nik/seagate_nik/bio_server. Native Orthrus batch condition scoring on packaged CHyMErA data produced condition_gene_calls.tsv and volcano/scatter plots, but combinatorial scoring still failed across tested parameter combinations with guide-ID/row-count errors and one missing %>% branch. Remains Production Blocked until an upstream-sanctioned combinatorial benchmark completes end to end. 2026-07-09T16:01:46+08:00 SOP promotion: Orthrus validated through Ubuntu runner API remote job 07a93bf9101a / Slurm job 593 using staged source /media/nik/seagate_nik/bio_server/repos/tools/orthrus and R library /media/nik/seagate_nik/bio_server/envs/tools/orthrus/Rlib. Added a real runner adapter that loads magrittr, dplyr, tidyr, and orthrus, runs packaged CHyMErA condition scoring for Torin_T12 versus HAP1_T12, then runs score_combn_vs_single with namespace-loaded tidyverse helpers and subset_to_matching_guide_id=FALSE. The final API run completed in 124.080 s and produced 92,746 input rows, 60,080 normalized rows, 4,806 condition gene calls, 688 combinatorial scored rows, 640 finite p-values/FDRs, min p-value 1.29198048979429e-33, min FDR 5.82070482792686e-30, differential range -2.55353579941789 to 1.74898354510585. Artifacts verified: summary.json, results.csv, orthrus_summary.csv, orthrus_combn_scored_data.csv, orthrus_condition_gene_calls.tsv, orthrus_result.json, orthrus_stdout.txt, orthrus_stderr.txt, slurm.out, and slurm.err.