guix-bioinformatics - Bioinformatics packages for GNU Guix

Age	Commit message (Collapse)	Author
3 days	Fixes after a recent guix pull	pjotrp

3 days	pylmm-gn2 moved to past	pjotrp

4 days	Packages reintroduced for GN	pjotrp

4 days	Moving failing packages out	pjotrp

5 days	Fixes to build	pjotrp

5 days	Fix (julia) packages by disabling tests (sorry)	pjotrp

5 days	Fixed (node) by removing dev dependencies before install	pjotrp

5 days	Drop unused GN and lizardfs packages	pjotrp

5 days	Fixes builds	pjotrp

5 days	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)
5 days	Moving to guix-bioinformatics-past	pjotrp

5 days	move patches	pjotrp

5 days	Removed (delly)	pjotrp

5 days	Mark RISC-V packages as obsolete	pjotrp

5 days	Continue cleanup	pjotrp

5 days	Delete older files	pjotrp

5 days	Moved redundant and older packages to new repo: guix-bioinformatics-past. It ↵	pjotrp
	may have been too much, but we can move back
5 days	Moving (genenetwork1, lisp) packages to guix-bioinformatics-past repo	pjotrp

6 days	update (pggb_) pggb 0.7.4 built successfully	pjotrp

6 days	Update (vg) to 1.72.0 and merged dev vg-gn package	pjotrp
	Summary of changes: - Merged vg-gn into vg (single package) - Updated version from 1.65.0 to 1.72.0 - Added openssl and wfa2-lib to inputs (new dependencies in 1.72.0) - Added libwfa2 to PKG_CONFIG_DEPS - Added subdirectory include paths (vcflib, fastahack, cairo, raptor2) via CPLUS_INCLUDE_PATH/C_INCLUDE_PATH - Fixed fastahack linking (use -lfastahack instead of adding .so to archive) - Fixed vcf2tsv test path to use (which "vcf2tsv") - Tests enabled and passing (1343/1343)
6 days	Fix (vg) v1.65.0 with vcflib build [AI]	pjotrp

6 days	Fix (vcflib) upgrade to latest 1.0.15	pjotrp
	Includes vcflib CMake patch that will be merged upstream.
6 days	Bump (vcflib) version to 1.0.15. Remove wfa2-lib-static package	pjotrp

7 days	fix (vcflib) zig support added back in	pjotrp

7 days	Updated (wfa2lib) to latest version and simplified package definition [AI]	pjotrp

7 days	simplify(vcflib): moving patches to main vcflib source tree [AI]	pjotrp

7 days	Added tests(vcflib)	pjotrp

7 days	Updated (vg) now uses last vcflib release without vendoring v1.0.7.	pjotrp
	Still, it would be good to fix the includes in vcflib itself.
7 days	python-build: Add new package definition.	Frederick Muriuki Muriithi

7 days	python-typing-inspection: Add new package definition.	Frederick Muriuki Muriithi

7 days	python-backoff: Add new package definition.	Frederick Muriuki Muriithi

7 days	python-annotated-doc: Add new package definition.	Frederick Muriuki Muriithi

7 days	python-oslex: Add new package definition.	Frederick Muriuki Muriithi

7 days	python-mslex: Add new package definition.	Frederick Muriuki Muriithi

7 days	Move wfa2-lib ahead of where it is used.	Arun Isaac

7 days	Deprecate wfmash 0.14 in favour of latest.	Arun Isaac

11 days	Add (R/shiny system containers) two system containers added for xushenglab [AI]	pjotrp
	Two R/shiny system containers added jumpsem and jumpshiny that we were running ad hoc
12 days	Add R packages for jumpshiny, Jumpsem_web	pjotrp
	Add package for vg that vendors in older vcflib - this will change soon.
2026-03-11	fix vcflib	pjotrp

2026-03-10	Use license:	pjotrp

2026-03-05	Import r-dendextend and r-gggenes for cosigt workflow	pjotrp

2026-02-27	Add liftoff.	Arun Isaac
	Change-Id: I8155083427bef2d4652e32e8b1f6a833bfd7c011
2026-02-27	Add python-parasail.	Arun Isaac
	Change-Id: I2002ccfc73ab5205b01a430f5be89e976b563765
2026-02-27	Add parasail.	Arun Isaac
	Change-Id: Ibd442b9414910bdb7566feb6c5f6523313ecbd16
2026-02-25	Import missing modules for python-curio.	Arun Isaac
	Change-Id: Ia5d581ed8b6d89351278dc116db4ac21382198b6
2026-02-25	Import (guix build-system pyproject).	Arun Isaac

2026-02-25	Add python-curio.	Arun Isaac
	Upstream removed python-curio.
2026-02-25	Import (gnu packages python-check) for python-nose.	Arun Isaac
	Upstream moved python-nose to (gnu packages python-check).
2026-02-25	Add vcflib.	Arun Isaac
	Guix upstream removed vcflib. This package is still broken. Nevertheless, we add it to prevent the channel from breaking.
2026-02-17	Update gfaffix to 0.2.1.	Arun Isaac
	We update gfaffix to 0.2.1 and move it to the new cargo-inputs style.