From 166af502196a33c540aa43dcfd190cf2c274fef8 Mon Sep 17 00:00:00 2001 From: zly <644706215@qq.com> Date: Sat, 17 Jan 2026 13:11:16 +0800 Subject: [PATCH] Move digger reproduction env to tools/reproduction/ - Moved bttoxin_digger_v5_repro to tools/reproduction/bttoxin_digger - Updated docker-compose.yml to point to the new location - This declutters the root directory while preserving the reproduction environment --- .../reproduction/bttoxin_digger}/AGENTS.md | 0 .../reproduction/bttoxin_digger}/README.md | 0 .../reproduction/bttoxin_digger}/README_CN.md | 0 .../reproduction/bttoxin_digger}/docker-compose.yml | 0 .../reproduction/bttoxin_digger}/docker/Dockerfile | 0 .../bttoxin_digger}/examples/COMPARE_REPORT.md | 0 .../bttoxin_digger}/examples/inputs/97-27.fna | 0 .../bttoxin_digger}/examples/inputs/C15.fna | 0 .../external_dbs/bt_toxin/db/bt_toxin.pdb | Bin .../external_dbs/bt_toxin/db/bt_toxin.phr | Bin .../external_dbs/bt_toxin/db/bt_toxin.pin | Bin .../external_dbs/bt_toxin/db/bt_toxin.pjs | 0 .../external_dbs/bt_toxin/db/bt_toxin.pot | Bin .../external_dbs/bt_toxin/db/bt_toxin.psq | Bin .../external_dbs/bt_toxin/db/bt_toxin.ptf | Bin .../external_dbs/bt_toxin/db/bt_toxin.pto | Bin .../external_dbs/bt_toxin/db/db_update.tar.gz | Bin .../external_dbs/bt_toxin/db/old/bt_toxin.phr | Bin .../external_dbs/bt_toxin/db/old/bt_toxin.pin | Bin .../external_dbs/bt_toxin/db/old/bt_toxin.psq | Bin .../bt_toxin/db/old/db_update-20221208.tar.gz | Bin ...acterial Pesticidal Protein Database20200730.pdf | Bin .../external_dbs/bt_toxin/seq/bt_toxin20200321 | 0 .../external_dbs/bt_toxin/seq/bt_toxin20200401 | 0 .../external_dbs/bt_toxin/seq/bt_toxin20200730.txt | 0 .../external_dbs/bt_toxin/seq/bt_toxin20210607.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20210802.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20211011.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20211227.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20220128.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20220609.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20221208.fas | 0 .../external_dbs/bt_toxin/seq/bt_toxin20251104.fas | 0 .../external_dbs/bt_toxin/seq/updateDB.py | 0 .../reproduction/bttoxin_digger}/pixi.lock | 0 .../reproduction/bttoxin_digger}/pixi.toml | 0 .../reproduction/bttoxin_digger}/run_digger_pixi.sh | 0 37 files changed, 0 insertions(+), 0 deletions(-) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/AGENTS.md (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/README.md (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/README_CN.md (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/docker-compose.yml (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/docker/Dockerfile (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/examples/COMPARE_REPORT.md (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/examples/inputs/97-27.fna (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/examples/inputs/C15.fna (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.pdb (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.phr (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.pin (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.pjs (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.pot (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.psq (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.ptf (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/bt_toxin.pto (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/db_update.tar.gz (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/old/bt_toxin.phr (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/old/bt_toxin.pin (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/old/bt_toxin.psq (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/db/old/db_update-20221208.tar.gz (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/Bacterial Pesticidal Protein Database20200730.pdf (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20200321 (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20200401 (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20200730.txt (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20210607.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20210802.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20211011.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20211227.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20220128.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20220609.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20221208.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/bt_toxin20251104.fas (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/external_dbs/bt_toxin/seq/updateDB.py (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/pixi.lock (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/pixi.toml (100%) rename {bttoxin_digger_v5_repro => tools/reproduction/bttoxin_digger}/run_digger_pixi.sh (100%) diff --git a/bttoxin_digger_v5_repro/AGENTS.md b/tools/reproduction/bttoxin_digger/AGENTS.md similarity index 100% rename from bttoxin_digger_v5_repro/AGENTS.md rename to tools/reproduction/bttoxin_digger/AGENTS.md diff --git a/bttoxin_digger_v5_repro/README.md b/tools/reproduction/bttoxin_digger/README.md similarity index 100% rename from bttoxin_digger_v5_repro/README.md rename to tools/reproduction/bttoxin_digger/README.md diff --git a/bttoxin_digger_v5_repro/README_CN.md b/tools/reproduction/bttoxin_digger/README_CN.md similarity index 100% rename from bttoxin_digger_v5_repro/README_CN.md rename to tools/reproduction/bttoxin_digger/README_CN.md diff --git a/bttoxin_digger_v5_repro/docker-compose.yml b/tools/reproduction/bttoxin_digger/docker-compose.yml similarity index 100% rename from bttoxin_digger_v5_repro/docker-compose.yml rename to tools/reproduction/bttoxin_digger/docker-compose.yml diff --git a/bttoxin_digger_v5_repro/docker/Dockerfile b/tools/reproduction/bttoxin_digger/docker/Dockerfile similarity index 100% rename from bttoxin_digger_v5_repro/docker/Dockerfile rename to tools/reproduction/bttoxin_digger/docker/Dockerfile diff --git a/bttoxin_digger_v5_repro/examples/COMPARE_REPORT.md b/tools/reproduction/bttoxin_digger/examples/COMPARE_REPORT.md similarity index 100% rename from bttoxin_digger_v5_repro/examples/COMPARE_REPORT.md rename to tools/reproduction/bttoxin_digger/examples/COMPARE_REPORT.md diff --git a/bttoxin_digger_v5_repro/examples/inputs/97-27.fna b/tools/reproduction/bttoxin_digger/examples/inputs/97-27.fna similarity index 100% rename from bttoxin_digger_v5_repro/examples/inputs/97-27.fna rename to tools/reproduction/bttoxin_digger/examples/inputs/97-27.fna diff --git a/bttoxin_digger_v5_repro/examples/inputs/C15.fna b/tools/reproduction/bttoxin_digger/examples/inputs/C15.fna similarity index 100% rename from bttoxin_digger_v5_repro/examples/inputs/C15.fna rename to tools/reproduction/bttoxin_digger/examples/inputs/C15.fna diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pdb b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pdb similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pdb rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pdb diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.phr b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.phr similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.phr rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.phr diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pin b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pin similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pin rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pin diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pjs b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pjs similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pjs rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pjs diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pot b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pot similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pot rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pot diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.psq b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.psq similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.psq rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.psq diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.ptf b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.ptf similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.ptf rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.ptf diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pto b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pto similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/bt_toxin.pto rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pto diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/db_update.tar.gz b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/db_update.tar.gz similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/db_update.tar.gz rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/db_update.tar.gz diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.phr b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.phr similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.phr rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.phr diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.pin b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.pin similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.pin rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.pin diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.psq b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.psq similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/bt_toxin.psq rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/bt_toxin.psq diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/db_update-20221208.tar.gz b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/db_update-20221208.tar.gz similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/db/old/db_update-20221208.tar.gz rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/old/db_update-20221208.tar.gz diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/Bacterial Pesticidal Protein Database20200730.pdf b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/Bacterial Pesticidal Protein Database20200730.pdf similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/Bacterial Pesticidal Protein Database20200730.pdf rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/Bacterial Pesticidal Protein Database20200730.pdf diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200321 b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200321 similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200321 rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200321 diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200401 b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200401 similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200401 rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200401 diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200730.txt b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200730.txt similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20200730.txt rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20200730.txt diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20210607.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20210607.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20210607.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20210607.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20210802.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20210802.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20210802.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20210802.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20211011.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20211011.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20211011.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20211011.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20211227.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20211227.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20211227.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20211227.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20220128.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20220128.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20220128.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20220128.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20220609.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20220609.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20220609.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20220609.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20221208.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20221208.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20221208.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20221208.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20251104.fas b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20251104.fas similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/bt_toxin20251104.fas rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/bt_toxin20251104.fas diff --git a/bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/updateDB.py b/tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/updateDB.py similarity index 100% rename from bttoxin_digger_v5_repro/external_dbs/bt_toxin/seq/updateDB.py rename to tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/updateDB.py diff --git a/bttoxin_digger_v5_repro/pixi.lock b/tools/reproduction/bttoxin_digger/pixi.lock similarity index 100% rename from bttoxin_digger_v5_repro/pixi.lock rename to tools/reproduction/bttoxin_digger/pixi.lock diff --git a/bttoxin_digger_v5_repro/pixi.toml b/tools/reproduction/bttoxin_digger/pixi.toml similarity index 100% rename from bttoxin_digger_v5_repro/pixi.toml rename to tools/reproduction/bttoxin_digger/pixi.toml diff --git a/bttoxin_digger_v5_repro/run_digger_pixi.sh b/tools/reproduction/bttoxin_digger/run_digger_pixi.sh similarity index 100% rename from bttoxin_digger_v5_repro/run_digger_pixi.sh rename to tools/reproduction/bttoxin_digger/run_digger_pixi.sh