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Rename to toolbox-assets and point the manifest at the new URLs #2

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Merged
edkerk merged 1 commit into from
Oct 17, 2026
Merged

Rename to toolbox-assets and point the manifest at the new URLs #2

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21 changes: 13 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
@@ -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.

Expand All @@ -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.
Expand Down Expand Up @@ -64,9 +69,9 @@ python scripts/build_binary_bundles.py # -> dist/binaries/*.zip (from RAV
python scripts/build_kegg_artefacts.py ... # -> kegg<NNN>_*.{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 <kegg 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 <kegg 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
Expand Down
32 changes: 16 additions & 16 deletions manifest.json
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Expand Up @@ -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
}
Expand All @@ -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
}
Expand All @@ -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
}
Expand All @@ -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
}
Expand All @@ -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
}
Expand Down