From 0d7f3be1c77d935016019f1f60992eb512aa5f94 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 16 Oct 2026 00:12:44 +0200 Subject: [PATCH] Rename to toolbox-assets and point the manifest at the new URLs --- README.md | 21 +++++++++++++-------- manifest.json | 32 ++++++++++++++++---------------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 341ea0d..1820e74 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,21 @@ -# raven-data +# toolbox-assets Downloadable **data artefacts and external-tool binaries** for -[RAVEN](https://github.com/SysBioChalmers/RAVEN) (MATLAB) and -[raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox) (Python). +[RAVEN](https://github.com/SysBioChalmers/RAVEN) (MATLAB), +[raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox) (Python), +[GECKO](https://github.com/SysBioChalmers/GECKO) (MATLAB) and +[geckopy](https://github.com/SysBioChalmers/geckopy) (Python). This repository hosts the large files those tools fetch on demand — KEGG reference data, prebuilt HMM libraries, and the BLAST+/DIAMOND/HMMER binaries — as **GitHub Release assets**, indexed by a single [`manifest.json`](manifest.json). Keeping them here (instead of attached to the code repositories) keeps the code releases clean, -isolates the assets' upstream licenses, and gives both the MATLAB and Python tools +isolates the assets' upstream licenses, and gives the MATLAB and Python tools one shared, versioned source of truth. +It was `SysBioChalmers/raven-data` until October 2026; GitHub redirects the old +URLs here. + > The HMM libraries are ~135–155 MB each — past GitHub's 100 MB per-file git limit — > so they can only live as release assets, never committed into a repo's tree. @@ -31,7 +36,7 @@ Windows), `kegg118`. An asset is uploaded **once** under its tag and **never re-uploaded**. When a tool bumps (say DIAMOND → 2.1.18) you publish a *new* tag `diamond-2.1.18` with only that tool's ZIPs; every other tag is untouched. -There is **no single "raven-data version"**. The role of "a snapshot of the whole +There is **no single "toolbox-assets version"**. The role of "a snapshot of the whole set" is played by **`manifest.json`** (tiny text), versioned as `manifest-v1`, `manifest-v2`, … — bumped only when the *pointer set* changes. The binaries themselves are stored once and merely re-referenced across manifest versions. @@ -64,9 +69,9 @@ python scripts/build_binary_bundles.py # -> dist/binaries/*.zip (from RAV python scripts/build_kegg_artefacts.py ... # -> kegg_*.{tar.gz,hmm.gz,gz} # upload to this repo's releases (idempotent; skips assets already present): -python scripts/publish_to_raven_data.py binaries --dir dist/binaries -python scripts/publish_to_raven_data.py release --tag kegg118 --dir -python scripts/publish_to_raven_data.py release --tag manifest-v1 data/manifest.json +python scripts/publish_to_toolbox_assets.py binaries --dir dist/binaries +python scripts/publish_to_toolbox_assets.py release --tag kegg118 --dir +python scripts/publish_to_toolbox_assets.py release --tag manifest-v1 data/manifest.json ``` See `docs/maintenance/maintaining_binaries.md` and `maintaining_kegg_data.md` in diff --git a/manifest.json b/manifest.json index bd1ba03..76475dc 100644 --- a/manifest.json +++ b/manifest.json @@ -6,25 +6,25 @@ "version": "kegg118", "description": "KEGG reference model + KO/reaction tables (core bundle), taxonomy, and prokaryote/eukaryote HMM libraries for getKEGGModelForOrganism.", "license": "Derived from the KEGG database; redistributed with permission from KEGG.", - "source": "https://github.com/SysBioChalmers/raven-data/releases/tag/kegg118", + "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/kegg118", "files": { "kegg118_core.tar.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_core.tar.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", "sha256": "520ba8bb09d6ca479ca1ab84ea70bf7c1d7f82d8f6406b717cee293b7c8609ca", "bytes": 49049340 }, "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", "sha256": "05999a38f3a1a5186d19d4e415f5029c33af56a08edb75190bd98ea19437765a", "bytes": 135087358 }, "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", "sha256": "ff9f25389e4c9c1cd58c13ee8d48d68a23152d04761d2e5875a9b5de8051b7b4", "bytes": 154511741 }, "kegg118_taxonomy.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_taxonomy.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", "sha256": "5499c9537ac2697592dd1b484f309027509472e25a9d39d925dc581b9eef46e2", "bytes": 228754 } @@ -34,10 +34,10 @@ "version": "0.2", "description": "WoLFPSORT subcellular-localization predictor (RAVEN getWoLFScores). Whole-tree bundle (perl + data + Linux i386 static binaries), extracted into software/WoLFPSORT/.", "license": "WoLFPSORT (Horton et al.); see the LICENSE inside the bundle.", - "source": "https://github.com/SysBioChalmers/raven-data/releases/tag/wolfpsort-0.2", + "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/wolfpsort-0.2", "files": { "wolfpsort-0.2.zip": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/wolfpsort-0.2/wolfpsort-0.2.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/wolfpsort-0.2/wolfpsort-0.2.zip", "sha256": "d37829b8c5c9128decbcf633dbde194d5ccdb9ae6ffde6c2089093f4c65161ce", "bytes": 7848573 } @@ -53,17 +53,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", "sha256": "c887deae9f3ac85bb5a0bbbf9af254d00f3bebf9764304a9582db39e1c843085", "bytes": 25262842 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", "sha256": "f1ff0b9e718fbb252d240e31e4f85f842f6ef8e99a0e97bf5f66390295c795da", "bytes": 35244129 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", "sha256": "b80d6ee1c1f85b8c18ae009e7d2ee844738d1a17338928570f5113ecd16e8326", "bytes": 13016674 } @@ -78,17 +78,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", "sha256": "6e432f8b205fb14c355c330cd4d802acb7decaaf17cfbe90573c614b6dc976c8", "bytes": 8968841 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", "sha256": "3f929c151b8d8061391d73510b2011e9c8820fa5e2b6b9ae142c3b4dfccced5d", "bytes": 6476740 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", "sha256": "daabab3d6072f4a37e701a5e02944f0fbcf8791ae5daa125fb7b5daed4a9be6d", "bytes": 3341980 } @@ -103,17 +103,17 @@ ], "platforms": { "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", "sha256": "19ce00c5dcdead0cdcb1f89cfafac299521afa79296e9a671baf73a64b7385eb", "bytes": 1802736 }, "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", "sha256": "d60e6b4bead44cf6d0cbd5711f9bda4a11cf72d7db07545ee0a43160b60b9fac", "bytes": 215961 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", "sha256": "89596237e4a6a325a5f8526983696a1197e6970b1352db81a9817a165cd62f82", "bytes": 339284 }