[med-svn] [Git][med-team/barrnap][master] add TODO for new upstream
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Sat Oct 17 07:33:48 BST 2026
Sascha Steinbiss pushed to branch master at Debian Med / barrnap
Commits:
5a410c95 by Sascha Steinbiss at 2026-10-17T08:33:09+02:00
add TODO for new upstream
This is a major change and will require some dedication.
Adding a TODO with some pointers from Debian Inference Server.
- - - - -
1 changed file:
- + debian/TODO
Changes:
=====================================
debian/TODO
=====================================
@@ -0,0 +1,129 @@
+barrnap packaging TODO for the 1.10.x upstream rewrite
+=====================================================
+
+Upstream 1.10.x is a near-complete rewrite of barrnap (after an 8-year gap).
+HMMER/nhmmer is replaced by Infernal covariance models, the kingdom set
+changed (bac/arc/fun; euk and mito are gone), the databases are no longer
+shipped, and barrnap now annotates all microbial RNA (rRNA/tRNA/tmRNA/
+ncRNA/mRNA/RBS/CDS/sig_pep/terminator) via several external tools.
+
+
+VERSION
+-------
+- The latest upstream *release* on GitHub is v1.10.5 (Apr 2026); the local
+ git tag upstream/1.10.6 has no corresponding upstream release and the
+ script's $VERSION still reads "1.10.5". Use 1.10.5-1, or wait for an
+ upstream 1.10.6 that bumps the version string.
+- Update debian/changelog with the new revision once decided.
+
+
+BLOCKERS
+--------
+1. Databases are not shipped.
+ db/{arc,bac,fun}/ contain only database.yml; the .cm (covariance models)
+ and .dmnd (diamond protein DBs) must be built via build/Makefile, which
+ downloads Rfam.cm.gz (~1GB), UniProt/SwissProt, and NCBI taxonomy and
+ requires cmfetch, cmpress, diamond, mmseqs, seqkit, taxonkit. This
+ cannot run during a Debian build (no network access).
+ => Produce a +dfsg tarball with pre-built .cm/.dmnd files (built in a
+ network-enabled environment), OR ship a separate barrnap-data package.
+ Update debian/watch dversionmangle accordingly.
+
+2. Three runtime dependencies are not packaged in Debian (trixie):
+ taxonkit - NOT in archive (also a build-time dep for the DBs)
+ pyrodigal - NOT in archive (no CLI; only python3-pyrodigal would be
+ the Python module, and it isn't packaged either)
+ ziggypep - NOT in archive
+ require_exe() is called unconditionally before any input processing, so
+ barrnap will refuse to start without all three.
+ => File ITP bugs / package them, OR patch upstream to make them optional
+ (they are only needed for the --all mRNA path).
+
+ Confirmed-available deps:
+ infernal (1.1.5-3), aragorn (1.2.41-3), any2fasta (0.4.2-2; upstream
+ wants >=0.6.0 - check -k flag), seqkit (2.9.0), diamond-aligner
+ (2.1.11-2, provides /usr/bin/diamond), transtermhp (2.09-5, provides
+ transterm), make, bedtools, mmseqs2 (for DB build), libpath-tiny-perl,
+ libfile-which-perl, liblist-moreutils-perl.
+
+
+PATCHES (both currently fail to apply - verified with patch --dry-run)
+----------------------------------------------------------------------
+- use_debian_dirs: code changed from
+ my $DBDIR = "$FindBin::RealBin/../db";
+ to
+ my $DEFAULT_DBDIR = path("$FindBin::RealBin/../db")->realpath;
+ The shebang env->/usr/bin/perl part still applies; the DBDIR fallback
+ must be rewritten against $DEFAULT_DBDIR.
+- deterministic_output.patch: the patched line
+ join(' ', values %KINGDOM)
+ no longer exists; the new code uses @KINGDOM (a qw array, already
+ deterministic). DROP this patch.
+- Update debian/patches/series accordingly.
+
+
+debian/control
+--------------
+- Build-Depends: drop lua5.1, hmmer. Add libpath-tiny-perl,
+ libfile-which-perl, liblist-moreutils-perl (needed so help2man can run
+ bin/barrnap --help).
+- Depends: drop hmmer. Add infernal, aragorn, any2fasta, seqkit,
+ transtermhp, diamond-aligner, make, libpath-tiny-perl,
+ libfile-which-perl, liblist-moreutils-perl, plus the 3 unpackaged tools
+ once they exist.
+- Description: package now annotates all microbial RNA, not just rRNA;
+ consider updating the long description.
+
+
+debian/rules
+------------
+- help2man --name says "Predict location of ribosomal RNA genes"; upstream
+ $DESC is now "Rapid microbial RNA annotation". Align.
+- If shipping pre-built DBs via +dfsg, verify debian/barrnap.install picks
+ up db/{arc,bac,fun}/*.cm and *.dmnd. Decide whether to install build/.
+
+
+debian/tests/test-example (completely broken - needs rewrite)
+--------------------------------------------------------------
+- Uses --kingdom euk and --kingdom mito (removed; only bac/arc/fun exist).
+- References examples/*.fna (examples/ is gone; test data is now in test/).
+- Rewrite to use valid kingdoms and test/{small,bac,arc,fun}.fa.
+
+
+debian/tests/control
+--------------------
+- Comment references hmmer; update to infernal + new deps.
+- Re-evaluate Architecture: line based on which deps are available where.
+
+
+debian/copyright
+----------------
+- db/* license: .dmnd files derive from UniProt SwissProt (CC-BY-4.0), so
+ the db/* stanza (currently CC0-1.0 only) must cover Rfam (CC0) and
+ UniProt-derived data. Reference LICENSE.Rfam.
+- Files: debian/* year -> 2014-2026.
+
+
+debian/watch
+------------
+- Points to github.com/Victorian-Bioinformatics-Consortium/barrnap/tags,
+ but copyright/upstream metadata use github.com/tseemann/barrnap.
+ Canonical repo is tseemann/barrnap; align. Keep/adjust dversionmangle
+ if using +dfsg.
+
+
+debian/upstream/metadata
+-------------------------
+- Verify Repository/Repository-Browse/Bug-* URLs (tseemann/barrnap).
+
+
+CLEANUP
+-------
+- Remove debian/filter_hmms.lua (obsolete; was for old .hmm filtering).
+
+
+GENERAL
+-------
+- Once done, fold the permanent parts (how the +dfsg tarball is made, how
+ databases are built/shipped, how the quilt patches work) into
+ debian/README.source. Keep transient findings in debian/changelog.
View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/commit/5a410c951c1b3c73c549709e0c83095cc838ae72
--
View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/commit/5a410c951c1b3c73c549709e0c83095cc838ae72
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