| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 4 days | gn: Add python-pyux. HEAD master | 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 | |
| 2025-10-22 | Genenetwork2: Upgrade to commit f0daa14. | Frederick Muriuki Muriithi | |
| 2025-10-20 | Genenetwork2: Upgrade to commit b3f5580. | Frederick Muriuki Muriithi | |
| 2025-10-15 | Genenetwork2: Upgrade to commit 3afc2ee. | Frederick Muriuki Muriithi | |
| 2025-10-15 | Genenetwork2: Upgrade to commit 24ee4c1. | Frederick Muriuki Muriithi | |
| 2025-10-14 | Remove phase: bin/genenetwork2 script no longer exists. | Frederick Muriuki Muriithi | |
| 2025-10-13 | gn-uploader: Upgrade to commit ea7d74d. | Frederick Muriuki Muriithi | |
| 2025-10-13 | gn-uploader: upgrade to commit c2b9306. | Frederick Muriuki Muriithi | |
| 2025-10-06 | genenetwork2: upgrade to commit e00d5ad. | Frederick Muriuki Muriithi | |
| 2025-10-06 | genenetwork2: upgrade to commit 7add12a. | Frederick Muriuki Muriithi | |
| 2025-10-06 | genenetwork3: Upgrade to commit d24ffc9. | Frederick Muriuki Muriithi | |
| 2025-10-06 | gn-auth: Upgrade to commit 9839e5b. | Frederick Muriuki Muriithi | |
| 2025-10-06 | python2-six: import from (past packages python27) | Frederick Muriuki Muriithi | |
| python2-six was deleted on mainline guix and moved to guix-past. | |||
| 2025-10-06 | guix-past: Update channel commit. | Frederick Muriuki Muriithi | |
| 2025-10-06 | python-unittest2: Copy deleted package over from guix mainline | Frederick Muriuki Muriithi | |
| Certain packages in guix-bioinformatics have `python-unittest2` as a dependency, but the package was deleted from guix mainline. This commit copies the deleted package definition over to guix-bioinformatics and includes the module where the package is used. | |||
| 2025-10-06 | python-nosexcover: Copy deleted package from mainline guix | Frederick Muriuki Muriithi | |
| Copy over the package deleted in mainline guix over to guix-bioinformatics. | |||
| 2025-10-06 | Upgrade dependency version: llvm 6 -> 12. | Frederick Muriuki Muriithi | |
| 2025-10-06 | Replace modules with the (past-crates packages crates-io) module | Frederick Muriuki Muriithi | |
| Replace the following rust modules with the (past-crates packages crates-io) where all the older rust packages were moved: * #:use-module (gnu packages crates-io) * #:use-module (gnu packages crates-check) * #:use-module (gnu packages crates-windows) * #:use-module (gnu packages crates-graphics) * #:use-module (gnu packages crates-compression) | |||
| 2025-10-06 | Add guix-rust-past-crates to list of channel dependencies. | Frederick Muriuki Muriithi | |
| Old rust packages have been removed from mainline guix and moved to the guix-rust-past-crates channel. This commit provides the channel giving access to the old packages. | |||
| 2025-10-06 | Remove obsolete dependencies | Frederick Muriuki Muriithi | |
| * python-pytest-cache: integrated into core python-pytest | |||
| 2025-10-06 | Replace tensorflow with tensorflow-lite. | Frederick Muriuki Muriithi | |
| The package `tensorflow` no longer exists on mainline guix, and it seems to have been replaced by `tensorflow-lite`. This commit updates the packages with `tensorflow` as a dependency to instead depend on `tensorflow-lite`. | |||
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index : guix-bioinformatics | |
| Bioinformatics packages for GNU Guix |
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