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2025-08-20Pass in the UID and GID under which the pola wrapper should run. change-working-dirs-to-tmpFrederick Muriuki Muriithi
2025-08-20Provide runtime directory path to each 'least-authority-wrapper'.Frederick Muriuki Muriithi
2025-08-19Change working directories for shepherd services to /tmp.Frederick Muriuki Muriithi
2025-08-19Setup permissions for runtime directories.Frederick Muriuki Muriithi
2025-08-19Create runtime directories for the different services.Frederick Muriuki Muriithi
2025-08-19Update module for nss-certs.Frederick Muriuki Muriithi
2025-08-18Revert "virtuoso-ose: patch in a temporary fix."Frederick Muriuki Muriithi
This reverts commit bffba8363575af62770875e0b70d040aacaf6730. 'virtuoso-ose' has been updated on mainline guix, so we no longer have to use our temporary version.
2025-08-16virtuoso-ose: patch in a temporary fix.Frederick Muriuki Muriithi
2025-08-16Add GN_GUILE_SERVER_URLMunyoki Kilyungi
2025-08-16genenetwork-development: Add gn-guile forge-project.Munyoki Kilyungi
* genenetwork-development.scm (genenetwork-projects): Add gn-guile.
2025-08-16genenetwork-development: Add missing guile port.Munyoki Kilyungi
* genenetwork-development.scm (genenetwork-shepherd-services): Add gn-guile-port.
2025-08-16genenetwork-development: Add gn-guile to sudoers file.Munyoki Kilyungi
* genenetwork-development.scm (operating-sytem) [sudoers-file]: Add gn-guile.
2025-08-16genenetwork-development: <genenetwork-configuration>: New field.Munyoki Kilyungi
* genenetwork-development.scm (<genenetwork-configuration>) [gn-guile-repository]: New field.
2025-08-16genenetwork-development: Run gn-guile from gn-guile git path.Munyoki Kilyungi
2025-08-11Publish channel as either 'gn-bioinformatics or 'guix-bioinformaticsFrederick Muriuki Muriithi
* Either name is acceptable.
2025-08-11Revert "virtuoso-ose: patch in a temporary fix."Frederick Muriuki Muriithi
This reverts commit 6402ef859d0057ef4fa9b369dc26719a4c1def9f.
2025-08-07virtuoso-ose: patch in a temporary fix.Frederick Muriuki Muriithi
2025-08-07Provide missing config variable.Frederick Muriuki Muriithi
2025-07-22Override redis with a custom-redis that's not dependent on syslogd.Munyoki Kilyungi
2025-07-22Set path for lmdb.Munyoki Kilyungi
We currently use lmdb for storing genotype files.
2025-07-22Add curl and coreutil-minimal to %base-packages.Munyoki Kilyungi
This helps when troubleshooting issues from inside the dev container.
2025-07-22genenetwork-development: Set the profile and ssl-certs inside gexp.Munyoki Kilyungi
2025-07-22genenetwork-development: Set utf-8 chars in mysql socket.Munyoki Kilyungi
2025-07-22genenetwork-development: Set "TEST_FEATURE_SWITCH=True".Munyoki Kilyungi
2025-07-21gn-libs: Use HTTP(s) URI rather than local file pathsFrederick Muriuki Muriithi
Replace the local file path with a HTTP(s) URI in order to avoid problems with file permissions. This has the added benefit that the git server can be on a completely different (physical) host than the one that the CI/CD container runs in.
2025-07-21gn-auth: Use http(s) URI rather than local file path.Frederick Muriuki Muriithi
Use HTTP(s) URIs rather than local file paths in order to avoid problems with file permissions. Re-activate the webhook for gn-auth to allow manual triggering.
2025-07-21dev: issue tracker settingsArun Isaac
2025-01-15Replace repo URLs with "/home/git/public" for self-hosted setups.Munyoki Kilyungi
* genenetwork-development.scm (<genenetwork-configuration>): Replace "https://git.genenetwork.org" with "/home/git/public". * (genenetwork-projects)[gn-libs, gn-auth]{ci-jobs-trigger}: Delete. * (transform-genenetwork-database-project)[repository]: Replace "https://git.genenetwork.org" with "/home/git/public". * (transform-genenetwork-database-project)[repository]: Replace "https://git.genenetwork.org" with "/home/git/public". [ci-jobs-trigger]: Delete.
2025-01-06Add gn-libs to CI.Munyoki Kilyungi
2025-01-06Create a tmpdir for genenetwork2 tests.Munyoki Kilyungi
2025-01-06Add REQUESTS_CA_BUNDLE to genenetwork2 shepherd service.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-01-06Map "/tmp" in gn2/3 and make it writable.Munyoki Kilyungi
2025-01-06Explicitly set "RSCRIPT" in gn3 g-exp.Munyoki Kilyungi
2025-01-06Correctly delete virtuoso build directory.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database-gexp): Only delete virtuoso "build" directory.
2025-01-06Add gn-guile service to genenetwork-shepherd-services.Munyoki Kilyungi
* genenetwork-development-deploy.sh: share "/export/data/gn-docs/". * genenetwork-development.scm: Import gn-guile. (<genenetwork-configuration>)[gn-guile-port, gn-doc-git-checkout]: New fields. (gn-guile-gexp): New g-exp for running gn-guile. (genenetwork-shepherd-services): Add gn-guile service.
2025-01-06Set gn2 env variables inside the shepherd service.Munyoki Kilyungi
* genenetwork-development.scm: Import (guix search-paths). (genenetwork2-cd-gexp): Move environment variables ... (genenetwork-shepherd-services)[genenetwork2]: ... here.
2025-01-06Remove duplicate environment settings.Munyoki Kilyungi
* genenetwork-development.scm (genenetwork2-cd-gexp): Delete duplicate env settings that are later defined in "gn2.conf".
2024-12-06CI/CD: Update database URI - add socket path.Frederick Muriuki Muriithi
2024-11-12Add cron job for running transform-genenetwork-database-gexp.Munyoki Kilyungi
2024-11-12Delete %transform-genenetwork-database-export-directory.Munyoki Kilyungi
* genenetwork-development.scm (%transform-genenetwork-database-export-directory): Delete. (set-build-directory-permissions-gexp): Remove %transform-genenetwork-database-export-directory.
2024-11-12Rename transform-genenetwork-database.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database): Rename this to... (transform-genenetwork-database-project): ... this. (transform-genenetwork-database-project): Ditto.
2024-11-12Make %virtuoso-data-dir writeable by laminar.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-11-12Refactor ttl and data-loading into Virtuoso in ci job.Munyoki Kilyungi
* genenetwork-development.scm (transform-genenetwork-database): Use a script to generate and validate ttl files. (%connection-settings): New variable. Contains the sparql and mysql login credentials. (%virtuoso-data-dir): New variable. (transform-genenetwork-database-project): Update how the transform-genenetwork-database gexp is called. Add web hook.
2024-10-18Move directory permissions setting G-exp into separate variable.Arun Isaac
* genenetwork-development.scm (set-build-directory-permissions-gexp): New variable. * genenetwork-development.scm (operating-system)[services]: Use set-build-directory-permissions-gexp.
2024-10-18Provide UTF-8 locale so characters are encoded correctly.Munyoki Kilyungi
* genenetwork-development.scm (gn-gemtext-threads-project)[ci-jobs]: Set LC_ALL environment variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-10-18Explicitly set AUTH_SERVER_URL in gn3.conf.Munyoki Kilyungi
This fixes an issue where gn3 auth defaults to "auth.genenetwork.org" during query execution. Instead we explicitly set AUTH_SERVER_URL to "auth-cd.genenetwork.org"
2024-09-12Enable AI Search in GN2 CD.Munyoki Kilyungi
2024-06-19Replace tabs with white spaces.Munyoki Kilyungi
* genenetwork-development.scm: Run "M-x untabify".
2024-06-19Move xapian re-indexing checks into the indexing script.Munyoki Kilyungi
Let the python xapian indexing script check the checksums, instead of using a G-expression. This approach is simpler and more understandable; it is also more versatile and allows easier modification. * genenetwork-development.scm (build-xapian-index-cron-gexp): Use the indexing script to compare checksums. If the checksums changed, queue the genenetwork3-build-xapian-index laminar job. Co-authored-by: John Nduli <rookie101@jnduli.co.ke>
2024-06-17Configure CI for guile-lapack.Arun Isaac
* genenetwork-development.scm (guile-lapack-project): New variable. (operating-system)[services]{forge-service-type}: Add guile-lapack-project.
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-01-20 09:42:08 +0000