[med-svn] [Git][med-team/vg][master] Add overview of vg dependencies to package for Debian

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / vg


Commits:
80ddd730 by Andreas Tille at 2026-10-21T17:14:32+02:00
Add overview of vg dependencies to package for Debian

- - - - -


1 changed file:

- + debian/deps-to-package.md


Changes:

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debian/deps-to-package.md
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+# vg: dependencies to package for Debian
+
+Context: vg 1.78.0+ds no longer ships the bundled `deps/` submodules in the
+source tarball. The goal is to build vg against Debian-packaged dependencies
+only. This file records which upstream projects are still required to build
+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 |
+|---|---|---|
+| libsonlib | https://github.com/benedictpaten/sonLib | med-team/libsonlib |
+| libgbwt | https://github.com/jltsiren/gbwt | med-team/gbwt |
+| libgcsa2 | https://github.com/jltsiren/gcsa2 | med-team/gcsa2 |
+
+## C. Packaged in Debian, but vg uses a fork / newer snapshot (different fix)
+
+| Project | vg's dep (fork/snapshot) | Debian package |
+|---|---|---|
+| libsdsl | vgteam/sdsl-lite fork (newer snapshot; Debian libsdsl-dev is older and "fails many tests") | libsdsl-dev |
+| libssw | vgteam/Complete-Striped-Smith-Waterman-Library fork | libssw-dev (original upstream) |
+
+Fix for both: package/update to the vg fork rather than bundling.
+
+## Already packaged (no action)
+
+vcflib (libvcflib-dev), fastahack (libfastahack-dev), htslib (libhts-dev),
+libdeflate (libdeflate-dev), raptor2 (libraptor2-dev), sparsehash
+(libsparsehash-dev), jemalloc (libjemalloc-dev), lz4 (liblz4-dev),
+tsl-hopscotch-map (libtsl-hopscotch-map-dev), simde (libsimde-dev), mimalloc
+(libmimalloc-dev), BBHash (libbbhash-dev), backward-cpp
+(libbackward-cpp-dev), cairo (libcairo2-dev), pixman (libpixman-1-dev),
+elfutils (libdw-dev/libelf-dev), tabixpp (libtabixpp-dev - note: not yet in
+Build-Depends, needs adding).
+
+## Micro-libs not worth separate packaging
+
+Header-only / test / dev-only, generally bundled: lru_cache, ips4o, mio,
+atomic_queue, sparsepp, mmmultimap, sglib, sha1, bash-tap (test harness),
+FlameGraph (profiling scripts).
+
+## How these were identified
+
+Source of truth: `deps/` entries in the vg Makefile `LIB_DEPS` (linked
+libraries), plus `progress_bar`, `dozeu` (header) and `DYNAMIC` (header, built
+via cmake) which are compiled/copied into the build. Packaging status checked
+against Debian sid (apt) and salsa.debian.org (search for existing packaging
+repos).



View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/80ddd7301df82ea9335a6dcc51a5f9661d77bb6e

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View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/80ddd7301df82ea9335a6dcc51a5f9661d77bb6e
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