| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2026-03-20 | Deprecate wfmash 0.14 in favour of latest. | Arun Isaac | |
| 2026-03-16 | 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 | |||
| 2026-03-15 | 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. | |||
| 2026-02-16 | Add python-cfgraph. | Arun Isaac | |
| Upstream removed python-cfgraph. | |||
| 2026-02-16 | Replace python-consul with python-py-consul. | Arun Isaac | |
| Upstream deprecated python-consul in favor of python-py-consul. | |||
| 2026-02-16 | Import (gnu packages python-build) for python-six. | Arun Isaac | |
| Upstream moved python-six to (gnu packages python-build). | |||
| 2026-01-23 | gn: mummer: Update to 4.0.1. | Arun Isaac | |
| 2026-01-20 | gn: Add python-traceback2. | Arun Isaac | |
| python-traceback2 was removed from Guix upstream. | |||
| 2026-01-05 | gn: Add python-pyux. | Arun Isaac | |
| python-pyux was removed from Guix upstream. | |||
| 2025-12-21 | gn: Add moosefs so we can replace lizardfs on octopus | pjotrp | |
| * gn/packages/file-systems.scm (moosefs): New variable. | |||
| 2025-12-18 | gn: smoothxg: Update to 0.8.2. | Arun Isaac | |
| * gn/packages/bioinformatics.scm (smoothxg): Update to 0.8.2. | |||
| 2025-12-15 | Update guile sheepdog to 1426617. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-12-15 | Restore 'guix channel as dependency | Frederick Muriuki Muriithi | |
| Restore an unpinned 'guix channel as a dependency of this channel in an attempt to resolve issues with the automated build of the guix-bioinformatics channel in the genenetwork CI/CD system. | |||
| 2025-12-15 | Update guile-sheepdog to 1b2d120. | Munyoki Kilyungi | |
| 2025-12-15 | Add redis as a requirement for guile-sheepdog service. | Munyoki Kilyungi | |
| 2025-12-09 | Update gn-libs. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-12-09 | Add sheepdog as a service. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-12-09 | Add guile-sheepdog. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-12-01 | Import (gnu packages python-compression) for python-xopen. | Arun Isaac | |
| python-xopen has been moved to (gnu packages python-compression). | |||
| 2025-12-01 | gn: Add python-misaka | Arun Isaac | |
| python-misaka was removed from Guix upstream. | |||
| 2025-12-01 | gn: Add htslib-1.14. | Arun Isaac | |
| htslib-1.14 was removed from Guix upstream. | |||
| 2025-12-01 | gn: Add pbbam. | Arun Isaac | |
| pbbam was removed from Guix upstream. | |||
| 2025-12-01 | Do not depend on the guix and guix-forge channels. | Arun Isaac | |
| 2025-11-26 | Genenetwork3: Upgrade to commit e6c4457. | Frederick Muriuki Muriithi | |
| 2025-11-26 | Genenetwork2: Upgrade to commit 5e596f0. | Frederick Muriuki Muriithi | |
| 2025-11-25 | gn-uploader: Add rust-qtlreaper as a dependency. | Frederick Muriuki Muriithi | |
| After genotypes or phenotypes are uploaded/changed, we need to be able to run QTLReaper to update various pre-computed values in the database. We therefore need the presence of rust-qtlreaper for that. | |||
| 2025-11-24 | rust-qtlreaper: Upgrade to commit 4dafa72. | Frederick Muriuki Muriithi | |
| Update commit (and hash) after rebasing the rust-qtlreaper repo. | |||
| 2025-11-24 | rust-qtlreaper: Upgrade to commit abba408. | Alexander_Kabui | |
| * gn/packages/genenetwork.scm (rust-qtlreaper): Update to commit abba408. [source]: Use github URL from forked genenetwork rust-qtlreaper repo. | |||
| 2025-11-23 | gn: r-rrbgen: Disable tests. | Arun Isaac | |
| * gn/packages/bioinformatics.scm (r-rrbgen)[arguments]: Disable tests. | |||
| 2025-11-23 | Use correct introductory commit for the guix-rust-past-crates channel. | Arun Isaac | |
| 2025-11-18 | * Add: python-structlog to gn{-auth,gn2,3,-libs}. | Munyoki Kilyungi | |
| (genenetwork2): Add python structlog. (gn-auth): Ditto. (gn-libs): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-11-14 | Delete (gnu packages certs) | Munyoki Kilyungi | |
| This causes build failures when running: guix build -L ~/guix-bioinformatics/ ... | |||
| 2025-11-14 | gn-correlation: Upgrade to commit 48604d8. | Alexander_Kabui | |
| * gn/packages/crate-io.scm (gn-rust-correlation): Update to 48604d8. | |||
| 2025-11-05 | Remove quote. | Frederick Muriuki Muriithi | |
| 2025-11-05 | gn-uploader: Upgrade to commit c4494da. | Frederick Muriuki Muriithi | |
| 2025-11-03 | Fix guix-forge channel. | Frederick Muriuki Muriithi | |
| While we do not directly depend on guix-forge within guix-bioinformatics, our deployment does. Sometimes, pulling in the latest version of guix-forge leads to a failure to build the appropriate guix profiles to use to (re)build containers. This commit fixes a commit for guix-forge to be used for building: - packages in this system (guix-forge is not used for this) - Genenetwork's deployment (guix-forge is needed) Essentially, this commit works simply to keep track of compatible guix-forge commits for the guix (mainline) commit that we have chosen for guix-bioinformatics. | |||
| 2025-10-27 | Genenetwork2: Upgrade to commit e2f9e82. | Frederick Muriuki Muriithi | |
| 2025-10-27 | Genenetwork3: Upgrade to commit 019282e. | Frederick Muriuki Muriithi | |
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index : guix-bioinformatics | |
| Bioinformatics packages for GNU Guix |
| about summary refs log tree commit diff |