[med-svn] [Git][med-team/vg][master] Order the vg dependency packaging plan
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Oct 22 11:10:10 BST 2026
Andreas Tille pushed to branch master at Debian Med / vg
Commits:
156caefb by Andreas Tille at 2026-10-22T12:00:53+02:00
Order the vg dependency packaging plan
Arrange the remaining dependencies so each item can be built after the
items above it. Put libhandlegraph first because libgbwtgraph, libbdsg,
libxg and libvgio all need it and it does not depend on the packages
currently in NEW. Record that libsdsl is done, that libsonlib, libgbwt
and libgcsa2 are in NEW, and that libssw should be updated rather than
packaged as a second fork.
- - - - -
1 changed file:
- debian/deps-to-package.md
Changes:
=====================================
debian/deps-to-package.md
=====================================
@@ -8,41 +8,88 @@ vg but are not yet available as Debian packages.
Status snapshot: 2026-10-21, against vg 1.78.0+ds. Upstream HEAD commits were
recorded on this date (they move over time; verify before packaging).
-## A. Not packaged in Debian, no existing packaging repo (create new)
-
-| Debian project name | Upstream URL | Upstream HEAD (2026-10-21) |
-|---|---|---|
-| libhandlegraph | https://github.com/vgteam/libhandlegraph | 3d8c3c9b1e3f |
-| libbdsg | https://github.com/vgteam/libbdsg | 485b32ba4f21 |
-| libvgio | https://github.com/vgteam/libvgio | 54490c2bdbf3 |
-| libxg | https://github.com/vgteam/xg | 8dd476de924a |
-| libgssw | https://github.com/vgteam/gssw | 14b4d43736bb |
-| libpinchesandcacti | https://github.com/benedictpaten/pinchesAndCacti | 67138b54ccf4 |
-| libsublinear-ls | https://github.com/yoheirosen/sublinear-Li-Stephens | 602b9e9f1913 |
-| libstructures | https://github.com/vgteam/structures | 391e4f70074d |
-| libgfaz | https://github.com/babyplutokurt/GFAz | f1c1b7feab80 |
-| libgbwtgraph | https://github.com/jltsiren/gbwtgraph | d566db9df177 |
-| libkff (kff-cpp-api) | https://github.com/Kmer-File-Format/kff-cpp-api | cf4d866405a0 |
-| cpp-progress-bar (tool, linked into vg) | https://github.com/vgteam/cpp_progress_bar | 487bb7c9c5f0 |
-| libdozeu (header-only) | https://github.com/vgteam/dozeu | d0e9ba6c0833 |
-| libdynamic (header-only, cmake-built) | https://github.com/vgteam/DYNAMIC | 095dc9dba0e9 |
-
-## B. Not in Debian, but a Salsa packaging repo already exists (check before creating new)
-
-| Debian project name | Upstream URL | Existing Salsa repo | Remark |
-|---|---|---|
-| libsonlib | https://github.com/benedictpaten/sonLib | med-team/libsonlib | In new queue |
-| libgbwt | https://github.com/jltsiren/gbwt | med-team/gbwt | In new queue |
-| libgcsa2 | https://github.com/jltsiren/gcsa2 | med-team/gcsa2 | In new queue |
-
-## C. Packaged in Debian, but vg uses a fork / newer snapshot (different fix)
-
-| Project | vg's dep (fork/snapshot) | Debian package | Remark |
-|---|---|---|
-| libsdsl | vgteam/sdsl-lite fork (newer snapshot; Debian libsdsl-dev is older and "fails many tests") | libsdsl-dev | Upgraded to version 2.4 |
-| libssw | vgteam/Complete-Striped-Smith-Waterman-Library fork | libssw-dev (original upstream) | What is the difference between the fork? |
-
-Fix for both: package/update to the vg fork rather than bundling.
+## Packaging order
+
+The list is ordered so that each item can be built with the items above it
+plus libraries that are already in Debian. Items in the same group are
+independent of each other and can be worked on in parallel.
+
+### Group 0: done or already in NEW
+
+1. **libsdsl** — DONE (2.4). The existing Debian package was updated; vg no
+ longer needs the vgteam snapshot.
+2. **libsonlib** — existing Salsa repo `med-team/libsonlib`, in NEW.
+ https://github.com/benedictpaten/sonLib
+3. **libgbwt** — existing Salsa repo `med-team/gbwt`, in NEW; depends on
+ libsdsl and zstd, both already packaged.
+ https://github.com/jltsiren/gbwt
+4. **libgcsa2** — existing Salsa repo `med-team/gcsa2`, in NEW; depends on
+ libsdsl and libdivsufsort, both already packaged.
+ https://github.com/jltsiren/gcsa2
+
+### Group 1: foundational and independent libraries
+
+5. **libhandlegraph** — NEXT. It has no dependency on the remaining new
+ packages and is required by libgbwtgraph, libbdsg, libxg and libvgio.
+ Starting here also avoids waiting for the packages currently in NEW.
+ https://github.com/vgteam/libhandlegraph
+ (upstream HEAD 2026-10-21: `3d8c3c9b1e3f`)
+6. **libstructures** — no external dependencies.
+ https://github.com/vgteam/structures
+ (upstream HEAD 2026-10-21: `391e4f70074d`)
+7. **libgssw** — C library; needs only libm and zlib.
+ https://github.com/vgteam/gssw
+ (upstream HEAD 2026-10-21: `14b4d43736bb`)
+8. **libdozeu** — header-only; needs SIMDe, which is already packaged.
+ https://github.com/vgteam/dozeu
+ (upstream HEAD 2026-10-21: `d0e9ba6c0833`)
+9. **libdynamic** — header-only/CMake; needs tsl-hopscotch-map, which is
+ already packaged, and is required by libbdsg.
+ https://github.com/vgteam/DYNAMIC
+ (upstream HEAD 2026-10-21: `095dc9dba0e9`)
+10. **cpp-progress-bar** — header/tool compiled into vg; no dependencies.
+ https://github.com/vgteam/cpp_progress_bar
+ (upstream HEAD 2026-10-21: `487bb7c9c5f0`)
+11. **libkff** (kff-cpp-api) — no dependencies beyond the C++ standard
+ library. https://github.com/Kmer-File-Format/kff-cpp-api
+ (upstream HEAD 2026-10-21: `cf4d866405a0`)
+12. **libgfaz** — needs libzstd and OpenMP; no dependency on the other new
+ packages. https://github.com/babyplutokurt/GFAz
+ (upstream HEAD 2026-10-21: `f1c1b7feab80`)
+13. **libsublinear-ls** — needs htslib, liblzma, libbz2 and zlib, all already
+ packaged. https://github.com/yoheirosen/sublinear-Li-Stephens
+ (upstream HEAD 2026-10-21: `602b9e9f1913`)
+14. **libpinchesandcacti** — after libsonlib; builds 3EdgeConnected in its own
+ externalTools. https://github.com/benedictpaten/pinchesAndCacti
+ (upstream HEAD 2026-10-21: `67138b54ccf4`)
+15. **libssw** — already packaged in Debian. See the libssw note below; do not
+ create a second `libssw` package for the vg fork.
+
+### Group 2: vg-specific libraries
+
+16. **libgbwtgraph** — after libgbwt, libhandlegraph and libsdsl; also needs
+ OpenSSL and zstd. https://github.com/jltsiren/gbwtgraph
+ (upstream HEAD 2026-10-21: `d566db9df177`)
+17. **libbdsg** — after libhandlegraph and libdynamic; needs sdsl, jansson,
+ Boost and several already packaged header libraries.
+ https://github.com/vgteam/libbdsg
+ (upstream HEAD 2026-10-21: `485b32ba4f21`)
+18. **libxg** — after libhandlegraph and libsdsl; its remaining dependencies
+ are the bundled micro-headers. https://github.com/vgteam/xg
+ (upstream HEAD 2026-10-21: `8dd476de924a`)
+19. **libvgio** — after libhandlegraph; needs htslib, jansson and protobuf,
+ all already packaged. https://github.com/vgteam/libvgio
+ (upstream HEAD 2026-10-21: `54490c2bdbf3`)
+20. **vg** — after all of the above.
+
+### libssw note
+
+Debian already ships `libssw` 1.1. The vg "fork" is essentially upstream
+1.2.3 plus a SIMDe port and minor build/warning changes, not a separate
+implementation. Packaging it as another library would duplicate `libssw` and
+its SONAME. The better route is to update Debian's `libssw` to the current
+upstream release (1.2.5 or newer) or backport the newer C++ `Align(...,
+maskLen)` API that vg uses, then enable `use_packaged_ssw` in vg.
## Already packaged (no action)
View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/156caefb33d3c2f51122eff52eb8a63ae3bc45d5
--
View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/156caefb33d3c2f51122eff52eb8a63ae3bc45d5
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