guix-bioinformatics - Bioinformatics packages for GNU Guix

Age	Commit message (Collapse)	Author
11 hours	● All 29 packages in manifest.scm.example built successfully! No failures. HEAD main	pjotrp
	Including: - pangenomes (meta-package: 28 pangenome tools) - mempang-workshop (workshop meta-package: 20 direct + pangenomes) - 27 other workshop-related and GeneNetwork packages All test flag comments are in place, pafplot tests now run during build, and the manifest builds cleanly.
11 hours	Added (pangenomes) rtg-tools	pjotrp

12 hours	Add (pangenomes) gfalook	pjotrp

12 hours	Added (pangenome) pafplot	pjotrp

13 hours	Adding packages for the mempang workshop	pjotrp

32 hours	Mempang25 workshop	pjotrp

32 hours	Added bandageNG	pjotrp

33 hours	Added vg package back in	pjotrp

34 hours	Allow tuning rust packages	pjotrp

34 hours	Re-add vcflib package	pjotrp

5 days	pangenome: impg: updated to latest commit	pjotrp

5 days	Make tools tunable (pangenome)	pjotrp

6 days	Allow for tuning of C++ and Rust packages --tune=native	pjotrp

6 days	Make these pangenome packages tunable	pjotrp

6 days	New package (pangenomes) meta-package	pjotrp
	The pangenomes meta package propagates: wfmash, pggb, odgi, seqwish, smoothxg, impg, gfainject, gafpack, cosigt, minimap2, samtools, bedtools, bwa-mem2, meryl, kfilt, miniprot, pangene, gfaffix, gfautil, vcfbub, wally, fastga-rs, htslib
7 days	Rename channels.scm to avoid guix pull compilation error [AI]	pjotrp
	Rename manifest.scm to avoid guix pull compilation error [AI] Replace local-file with git-fetch statements
8 days	Propagate snakemake (cosigt)	pjotrp

8 days	Fix cosigt propagation for workflow and missing getopts in pggb	pjotrp

11 days	Add test (impg) integration test	pjotrp

12 days	Propagate fastga-rs in impg	pjotrp

12 days	Downgraded (wfmash) from 0.24 to 0.14. Pggb requires that. Cosigt tests:	pjotrp
	● ALL 12 STEPS PASS with wfmash-0.14! And note: Step 6 now shows 142 nodes (vs 7 nodes with wfmash-0.24) -- a much more detailed pangenome graph from pggb with the correct wfmash version. ● Genotype: sampleA#2#chr1 + sampleC#2#chr1, cosine similarity 0.52 -- exactly matching the expected result from the test README!
12 days	Update tests so they pass for cosigt	pjotrp

13 days	Add wfmash recent	pjotrp

13 days	Get pangenome tools going again	pjotrp

13 days	Working on cosigt and odgi (WIP)	pjotrp

2026-04-02	Enable tests (impg)	pjotrp

2026-04-02	Getting rid of guix-past dependency	pjotrp
	guix-bioinformatics is now fully self-contained -- no more guix-past or guix-rust-past-crates dependencies.
2026-04-02	Get rid of python-nose warning	pjotrp

2026-04-02	Updated (impg) to latest with dependencies	pjotrp

2026-04-02	Milestone achieved: guix-bioinformatics no longer depends on ↵	pjotrp
	guix-rust-past-crates. All Rust packages build with only -L . -L ../guix-past/modules.
2026-04-02	More surgery:	pjotrp
	- gn-rust-correlation moved to genenetwork-rust.scm with new-style cargo-inputs - crates-io.scm import removed from genenetwork.scm and bioinformatics.scm - past-crates is now only referenced by crates-io.scm itself (dead file) - genenetwork2 builds successfully - All Rust packages (rust-qtlreaper, gn-rust-correlation) build from their new locations
2026-04-02	Updated rust package for qtlreaper	pjotrp

2026-04-02	Move (gfaffix) to rust package	pjotrp

2026-04-02	Changed URLs for Chris packages	pjotrp

2026-04-02	Updated (gfautil) to latest rust packaging	pjotrp

2026-04-02	Moved all pangenome Rust packages to pangenome-rust.scm	pjotrp

2026-04-02	Added a number of packages for cosigt/impg:	pjotrp
	+ gfainject + rust-onecode + ragc + fastga-rs + spoa + impg gfautil + safestringlib + bwa-mem2 + miniprot + pangene + wally + meryl + kfilt + cosigt
2026-03-24	Fixes after a recent guix pull	pjotrp

2026-03-24	pylmm-gn2 moved to past	pjotrp

2026-03-23	Packages reintroduced for GN	pjotrp

2026-03-23	Moving failing packages out	pjotrp

2026-03-23	Fixes to build	pjotrp

2026-03-22	Fix (julia) packages by disabling tests (sorry)	pjotrp

2026-03-22	Fixed (node) by removing dev dependencies before install	pjotrp

2026-03-22	Drop unused GN and lizardfs packages	pjotrp

2026-03-22	Fixes builds	pjotrp

2026-03-22	fix (genenetwork2) build.	pjotrp
	Summary of fixes: - guix-rust-past-crates: All local-file "./patches/..." replaced with search-patches (10 patches across the file) - python-asserts: Disabled tests (#:tests? #f) - python-htmlgen: Disabled tests (#:tests? #f)
2026-03-22	Moving to guix-bioinformatics-past	pjotrp

2026-03-22	move patches	pjotrp

2026-03-22	Removed (delly)	pjotrp