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5 daysUpgrade guix channel to c84ba4f.•••* .guix-channel: Upgrade guix channel to c84ba4f. * gn/packages/crates-io.scm: Import (gnu packages crates-check) for rust-criterion. * gn/packages/crates-io.scm, gn/packages/bioinformatics.scm: Import (gnu packages crates-compression) for rust-flate2. Arun Isaac
12 daysgn: pggb: Use wfmash-0.14 instead of the latest wfmash.•••* gn/packages/bioinformatics.scm (pggb)[inputs]: Replace wfmash with wfmash-0.14. Arun Isaac
12 daysgn: Add wfmash-0.14.•••* gn/packages/bioinformatics.scm (wfmash-0.14): New variable. Arun Isaac
2025-02-11gn: pggb: Update to 0.7.2.•••* gn/packages/bioinformatics.scm (pggb): Update to 0.7.2. Arun Isaac
2025-02-11gn: pggb: Remove unused dependencies.•••These dependencies are referred to in the documentation and put into the Docker image, but are not actually used by pggb. * gn/packages/bioinformatics.scm (pggb)[inputs]: Remove fastix, mummer, pafplot and vcflib. Arun Isaac
2025-02-11gn: odgi: Disable tests.•••* gn/packages/bioinformatics.scm (odgi): Disable tests. Arun Isaac
2025-01-25gnu: r-rrbgen: Fix name typo.•••* gn/packages/bioinformatics.scm (r-rrbgen)[name]: Fix typo. Arun Isaac
2024-12-04gn: graphaligner: Update to 1.0.20.•••* gn/packages/bioinformatics.scm (graphaligner): Update to 1.0.20. [arguments]: Substitute in bamtools include directory. [inputs]: Add bamtools. Arun Isaac
2024-12-04gn: graphaligner: Use search-inputs-directory.•••* gn/packages/bioinformatics.scm (graphaligner)[arguments]: Use search-inputs-directory in patch-source phase. Arun Isaac
2024-12-03gnu: vg: Update to 1.61.0.•••* gn/packages/bioinformatics.scm (vg): Update to 1.61.0. [arguments]: Add #:make-flags. Create obj and lib directories, and prevent them from being deleted. Install libhandlegraph.so. Arun Isaac
2024-12-03gn: vg: Build man pages unconditionally.•••* gn/packages/bioinformatics.scm (vg)[arguments]: Build man pages unconditionally in the build-manpages phase. Arun Isaac
2024-12-03gn: vg: Use G-expressions.•••* gn/packages/bioinformatics.scm (vg): Use G-expressions. Arun Isaac
2024-12-03gn: vg: Remove commented-out code.•••* gn/packages/bioinformatics.scm (vg)[arguments]: Remove commented-out code. Arun Isaac
2024-10-25Upgrade guix channel to 2394a7f.•••* .guix-channel: Upgrade guix channel to 2394a7f. * gn/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl-static with (gsl "static"). * gn/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Replace gsl-static with (gsl "static"). * gn/packages/static.scm (wfmash-static)[inputs]: Replace gsl-static with (gsl "static"). Arun Isaac
2024-10-25gn: pplacer: Use G-expressions.•••* gn/packages/bioinformatics.scm (pplacer): Use G-expressions. Arun Isaac
2024-10-23gn: graphaligner: Update to 1.0.19.•••* gn/packages/bioinformatics.scm (graphaligner): Update to 1.0.19. [native-inputs]: Add (jemalloc "bin"). Arun Isaac
2024-10-23gn: graphaligner: Use G-expressions.•••* gn/packages/bioinformatics.scm (graphaligner): Use G-expressions. Arun Isaac
2024-10-22gn: smoothxg: Update to 0.8.0.•••* gn/packages/bioinformatics.scm (smoothxg): Update to 0.8.0. [arguments]: Remove architecture-specific -march=armv8-a+simd flag. Arun Isaac
2024-10-22gn: odgi: Update to 0.9.0.•••* gn/packages/bioinformatics.scm (odgi): Update to 0.9.0. Arun Isaac
2024-10-22gn: seqwish: Update to 0.7.11.•••* gn/packages/bioinformatics.scm (seqwish): Update to 0.7.11. Arun Isaac
2024-04-19gn: Add hifiasm.•••* gn/packages/bioinformatics.scm (hifiasm): New variable. Arun Isaac
2024-02-23gn: bioinformatics: Import (guix build-system r).Arun Isaac
2024-02-23gn: Add r-stitch.•••* gn/packages/bioinformatics.scm (r-stitch): New variable. Arun Isaac
2024-02-23gn: Add vcfpp.•••* gn/packages/bioinformatics.scm (vcfpp): New variable. Arun Isaac
2024-02-23gn: Add seqlib.•••* gn/packages/bioinformatics.scm (seqlib): New variable. Arun Isaac
2024-02-23gn: Add r-rrbgen.•••* gn/packages/bioinformatics.scm (r-rrbgen): New variable. Arun Isaac
2023-10-19Remove bh20-seq-resource.•••The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. * gn/packages/bioinformatics.scm (bh20-seq-resource): Delete variable. * gn/services/bh20-seq-resource-container.scm: Delete file. Arun Isaac
2023-09-26pggb: Add missing inputsEfraim Flashner
2023-09-26pggb: wrap with more packagesEfraim Flashner
2023-09-26gsl: Provide glibc-hwcaps version.Efraim Flashner
2023-09-26vg: Update package definitionEfraim Flashner
2023-09-26seqwish: Provide glibc-hwcaps versionEfraim Flashner
2023-09-26seqwish: Build and link against shared library.Efraim Flashner
2023-09-25seqwish: Make package tunable.Efraim Flashner
2023-09-25vg: Link with some shared libraries.Efraim Flashner
2023-09-24pggb: Fix typo.Efraim Flashner
2023-09-24pggb: Provide version with glibc-hwcaps.Efraim Flashner
2023-09-24smoothxg: Link with odgiEfraim Flashner
2023-09-24smoothxg: Link with sdsl-liteEfraim Flashner
2023-09-24seqwish: Link with sdsl-libEfraim Flashner
2023-09-24pggb: Remove python-pycairoEfraim Flashner
2023-09-24pggb: Add htslib for tabix dependency.Efraim Flashner
2023-09-22Add pggb.Efraim Flashner
2023-09-22vg: Prepare for using a shared library.Efraim Flashner
2023-09-22vg: Update to 1.50.0.Efraim Flashner
2023-09-21mummer: Update to 4.0.0rc1.Efraim Flashner
2023-09-21odgi: Add variant with glibc-hwcaps.Efraim Flashner
2023-09-21wfmash: Fix typos.Efraim Flashner
2023-09-21odgi: Update to 0.8.3.Efraim Flashner
2023-09-21Add smoothxgEfraim Flashner