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22 hoursgenenetwork2: Upgrade to commit 566dc1a. HEAD mainFrederick Muriuki Muriithi
22 hoursgenenetwork3: Upgrade to commit b3de4f5.Frederick Muriuki Muriithi
23 hoursgn-libs: Upgrade to commit 20e43c9.Frederick Muriuki Muriithi
7 daysSwitch guix-bioinformatics channel to its main branch.Arun Isaac
14 daysgn-uploader: upgrade to commit 3452472.Frederick Muriuki Muriithi
14 daysgn-guile: Fix indentations.Frederick Muriuki Muriithi
14 daysgn-guile: Modify phases to fix load paths.Frederick Muriuki Muriithi
14 daysgn-guile: Bump up PATCH version to force build of newer gn-guile.Frederick Muriuki Muriithi
14 daysgn-guile: Setup `HOME` and `USER` envvars.Frederick Muriuki Muriithi
The `gn-guile' service checks for configurations in the HOME directory and in the current working directory (CWD). If the HOME environment variable is not set, then `(getenv "HOME")' returns `#f' which causes an error to be raised in `guile-config' when it attempts to do `(string-append (getenv "HOME") ...)'. This commit ensures the HOME environment variable is set to prevent the error from occurring.
14 daysgn-guile: Replace envvars configs with CLI-argument configsFrederick Muriuki Muriithi
Remove the environment variable configs that are no longer used by the service, having moved to use of configuration files and command-line arguments to set up the service configurations.
14 daysgn-guile: Rename config to 'gn-doc-remote-uri'Frederick Muriuki Muriithi
Rename from 'gn-doc-git-checkout' to 'gn-doc-remote-uri' to make the name better elaborate on what the configuration is about.
14 daysgn-guile: Upgrade to commit d19fcd79.Frederick Muriuki Muriithi
This commit upgrades gn-guile to commit d19fcd79, which is the latest commit as at 2026-03-13T09:55CDT. It also adds the `guile-config` package as a dependency of gn-guile because the package is needed to assist with configuration of the service going forward.
2026-03-17gn-uploader: Upgrade to commit b39980e.Frederick Muriuki Muriithi
2026-03-05production: (gn-guile) Explicitly specify the working directory.Frederick Muriuki Muriithi
2026-03-05production: `operating-system': Update gn-guile/gn-docs configsFrederick Muriuki Muriithi
Expose the appropriate host directory to the container in read-write mode to enable the container make appropriate changes to the files. Tell the `operating-system' where to find the identity file and update the git configs to enable semi-automatic synchronisation of changes.
2026-03-05Refactor gn-guile-shepherd-serviceFrederick Muriuki Muriithi
* Remove the `ssh-command` and `guile-settings` variables
2026-03-05gn-guile: Refactor gn-guile-gexpFrederick Muriuki Muriithi
* Generate the GIT_SSH_COMMAND within the "inner" gexp * Return both the config, and the generated gexp
2026-03-05gn-guile: Set `GIT_COMMITTER*` envvars.Frederick Muriuki Muriithi
We need to set the `GIT_COMMITTER_NAME` and `GIT_COMMITTER_EMAIL` envvars to prevent the commit step from failing.
2026-03-05gn-guile: Disambiguate the working dir from the "remote" repo.Frederick Muriuki Muriithi
The assumption (before this commit) was that the bare/remote repository from which we'd clone the working repository was exposed to the container as a directory. The parent of that directory doubled as the working directory for the application. This conflation of purposes is wrong, and leads to problems, since the remote repo could be a URL/URI to an external service. This commit explicitly defines the working directory.
2026-03-05gn-guile: Upgrade to commit 5501745.Frederick Muriuki Muriithi
2026-03-05gn-guile: Add `openssh-sans-x` as a dependency.Frederick Muriuki Muriithi
Git needs the ssh command in order to successfully pull to or push/fetch from the remote.
2026-03-05gn-guile: Clone specific branch to use for synchronising with main.Frederick Muriuki Muriithi
2026-03-05gn-guile: Setup SSH configurationsFrederick Muriuki Muriithi
To enable successful cloning and pushing of repositories, we need to set up the identity file and some known hosts.
2026-03-05gn-guile: use (gn-machines genenetwork) not (gn packages guile).Frederick Muriuki Muriithi
2026-03-05gn-uploader: Change ownership of secrets directory and all its files.Frederick Muriuki Muriithi
2026-02-27Genenetwork2: Upgrade to commit ef4776e.Frederick Muriuki Muriithi
2026-02-25genenetwork2: Upgrade to commit 6e76271.Frederick Muriuki Muriithi
2026-02-16genenetwork2: Upgrade to commit d11c544.Frederick Muriuki Muriithi
2026-02-13gn-auth: Upgrade to commit 77b0316.Frederick Muriuki Muriithi
2026-02-12Add singularity installation scripts.Arun Isaac
2026-02-11gn-uploader: Upgrade to commit 1e1fa46.Frederick Muriuki Muriithi
2026-02-09gn-uploader: Upgrade to commit e3d8b80.Frederick Muriuki Muriithi
2026-02-09gn-uploader: Upgrade to commit 25e1047.Frederick Muriuki Muriithi
2026-02-09gn-auth: Upgrade to commit ca2fcbb.Frederick Muriuki Muriithi
2026-02-09gn-libs: Upgrade to commit a9d5cc0.Frederick Muriuki Muriithi
2026-02-07Expose sparql web-endpoint from container.Munyoki Kilyungi
2026-02-04gn-uploader: upgrade to commit b5a2b56.Frederick Muriuki Muriithi
2026-02-04genenetwork2: upgrade to commit 1aedd1d.Frederick Muriuki Muriithi
2026-01-30genenetwork2: Upgrade to commit 957c1ee.Frederick Muriuki Muriithi
2026-01-28Channel - guix-rust-past-crates: Fix the channel to commit b8b7ffb.Frederick Muriuki Muriithi
Fix the `guix-rust-past-crates` at a known working commit to prevent breakages due to any changes in the channel's repo.
2026-01-28Channel - guix-past: Fix the channel to commit 473c942.Frederick Muriuki Muriithi
There have been changes in the `guix-past` channels recently that have broken our builds. This commit fixes guix-past to a known working commit.
2026-01-28Reapply "Update .guix-channel."Frederick Muriuki Muriithi
Restores the changes introduced by @mbonz. The issues were caused by changes in upstream channels. This reverts commit aa6706d637e26ab447499b4558e734329ceeb19d.
2026-01-28Revert "Update .guix-channel."Frederick Muriuki Muriithi
The guix-bioinformatics commit 9b0955f leads to a cascade of breakages. I am thus reverting this commit to restore a previous sane state. This reverts commit 04c2a18f615bc0a387235544433989af2e8cb62b.
2026-01-27gn-uploader: Typo: UPLOAD_DIRECTORY --> UPLOADS_DIRECTORY.Frederick Muriuki Muriithi
2026-01-26gn-uploader: UPLOAD_FOLDER -> UPLOAD_DIRECTORYFrederick Muriuki Muriithi
Move the UPLOAD_DIRECTORY under the scratch directory and rename the configuration variable.
2026-01-26gn-uploader: Rename TEMPORARY_DIRECTORY to SCRATCH_DIRECTORYFrederick Muriuki Muriithi
Thinking of it as a scratch directory help us disassociate it from the /tmp directory, that we generally want to avoid using in the first place.
2026-01-15Add nginx block for "rdf.genenetwork.org".Munyoki Kilyungi
Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com>
2026-01-15Delete virtuoso schema visualization.Munyoki Kilyungi
For now this fails, and no one really uses it. Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com>
2026-01-15Set SPARQL endpoint env for gn-guile to render RDF pages.Munyoki Kilyungi
Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com>
2026-01-14Add "guix/" to prod container load path.Munyoki Kilyungi
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-04-02 13:26:11 +0000