| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2 days | pangenome: impg: updated to latest commit HEAD main | pjotrp | |
| 3 days | Make tools tunable (pangenome) | pjotrp | |
| 3 days | Allow for tuning of C++ and Rust packages --tune=native | pjotrp | |
| 3 days | Make these pangenome packages tunable | pjotrp | |
| 3 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 | |||
| 4 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 | |||
| 5 days | Propagate snakemake (cosigt) | pjotrp | |
| 5 days | Fix cosigt propagation for workflow and missing getopts in pggb | pjotrp | |
| 8 days | Add test (impg) integration test | pjotrp | |
| 9 days | Propagate fastga-rs in impg | pjotrp | |
| 9 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! | |||
| 9 days | Update tests so they pass for cosigt | pjotrp | |
| 10 days | Add wfmash recent | pjotrp | |
| 10 days | Get pangenome tools going again | pjotrp | |
| 10 days | Working on cosigt and odgi (WIP) | pjotrp | |
| 11 days | Enable tests (impg) | pjotrp | |
| 11 days | Getting rid of guix-past dependency | pjotrp | |
| guix-bioinformatics is now fully self-contained -- no more guix-past or guix-rust-past-crates dependencies. | |||
| 11 days | Get rid of python-nose warning | pjotrp | |
| 11 days | Updated (impg) to latest with dependencies | pjotrp | |
| 11 days | Milestone achieved: guix-bioinformatics no longer depends on ↵ | pjotrp | |
| guix-rust-past-crates. All Rust packages build with only -L . -L ../guix-past/modules. | |||
| 11 days | 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 | |||
| 11 days | Updated rust package for qtlreaper | pjotrp | |
| 11 days | Move (gfaffix) to rust package | pjotrp | |
| 11 days | Changed URLs for Chris packages | pjotrp | |
| 11 days | Updated (gfautil) to latest rust packaging | pjotrp | |
| 11 days | Moved all pangenome Rust packages to pangenome-rust.scm | pjotrp | |
| 11 days | 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 | |
| 2026-03-22 | Mark RISC-V packages as obsolete | pjotrp | |
| 2026-03-22 | Continue cleanup | pjotrp | |
| 2026-03-22 | Moved redundant and older packages to new repo: guix-bioinformatics-past. It ↵ | pjotrp | |
| may have been too much, but we can move back | |||
| 2026-03-22 | Moving (genenetwork1, lisp) packages to guix-bioinformatics-past repo | pjotrp | |
| 2026-03-22 | update (pggb_) pggb 0.7.4 built successfully | pjotrp | |
| 2026-03-22 | 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) | |||
| 2026-03-21 | Fix (vg) v1.65.0 with vcflib build [AI] | pjotrp | |
| 2026-03-21 | Fix (vcflib) upgrade to latest 1.0.15 | pjotrp | |
| Includes vcflib CMake patch that will be merged upstream. | |||
| 2026-03-21 | Bump (vcflib) version to 1.0.15. Remove wfa2-lib-static package | pjotrp | |
| 2026-03-21 | fix (vcflib) zig support added back in | pjotrp | |
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index : guix-bioinformatics | |
| Bioinformatics packages for GNU Guix |
| about summary refs log tree commit diff |