| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 44 hours | Expose sparql web-endpoint from container. HEAD main | Munyoki Kilyungi | |
| 2026-01-15 | Add nginx block for "rdf.genenetwork.org". | Munyoki Kilyungi | |
| Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com> | |||
| 2026-01-15 | Delete virtuoso schema visualization. | Munyoki Kilyungi | |
| For now this fails, and no one really uses it. Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com> | |||
| 2026-01-15 | Set SPARQL endpoint env for gn-guile to render RDF pages. | Munyoki Kilyungi | |
| Acked-by: Frederick Muriuki Muriithi <fredmanglis@gmail.com> | |||
| 2026-01-13 | Add sheepdog monitoring to dev container. | Munyoki Kilyungi | |
| 2026-01-13 | Search for gn3 modules first from GN3_PYTHONPATH. | Munyoki Kilyungi | |
| 2025-12-01 | Use genenetwork package variants from this channel. | Arun Isaac | |
| 2025-12-01 | Remove unused gn-libs import. | Arun Isaac | |
| 2025-11-14 | Manually create laminar profile directory if it doesn't exist. | Munyoki Kilyungi | |
| 2025-11-13 | Use latest Guix channel, not the commit with substitutes available. | Arun Isaac | |
| channel-with-substitutes-available only picks up on the commit with substitutes available when the container is built. That means we will be stuck with an old commit forever. This is not what we want. Better to pick the latest commit, and build it ourselves if substitutes aren't available. | |||
| 2025-11-12 | Adjust genetwork{2,3} reqs to not rely on gn-auth/genenetwork3. | Munyoki Kilyungi | |
| 2025-11-12 | Set the respawn limit for gn{-auth,2,3} to 5s from 0.5s. | Munyoki Kilyungi | |
| 2025-11-10 | Remove ccwl from development container. | Munyoki Kilyungi | |
| 2025-11-10 | Fix typo. | Munyoki Kilyungi | |
| 2025-11-10 | Make the {auth,llm}-db-path dir writable. | Munyoki Kilyungi | |
| 2025-11-10 | Set the correct home-directory when cloning repos in gn-guile g-exp. | Munyoki Kilyungi | |
| 2025-09-19 | Use /home/genenetwork for git cloning. | Munyoki Kilyungi | |
| 2025-09-19 | Set "genenetwork" user's home directory to /home/genenetwork. | Munyoki Kilyungi | |
| 2025-09-19 | Set the default GIT_PAGER to `cat`. | Munyoki Kilyungi | |
| 2025-09-19 | genenetwork-development: Make gn-docs repository persistent. | Munyoki Kilyungi | |
| Previously, gn-docs at `/export/data/repositories/gn-docs` was deleted and re-cloned on each service start, causing any local edits to be lost; now it is only cloned if missing, making it persistent across restarts so changes can be preserved. | |||
| 2025-09-19 | genenetwork-development: Map dir for auth-db-path instead of file. | Munyoki Kilyungi | |
| 2025-09-19 | genenetwork-development: Fix permissions for repository directories. | Munyoki Kilyungi | |
| * genenetwork-development.scm (genenetwork-service-type): Import (ice-9 ftw). Set top-level directories under REPOSITORIES to mode 0775 so they are writable by the "genenetwork" user/group. | |||
| 2025-09-19 | Set RSCRIPT from GN3_PROFILE env instead of development manifest. | Munyoki Kilyungi | |
| 2025-09-19 | Update gn2/gn3 shepherd-service dependencies. | Munyoki Kilyungi | |
| * genenetwork-development.scm (genenetwork-shepherd-services) [genenetwork2]: require redis gn-auth genenetwork3. [genenetwork3]: require gn-auth. | |||
| 2025-09-19 | Set environment variables for GN2. | Munyoki Kilyungi | |
| 2025-09-19 | Remove use of the "bin/genenetwork2" script. | Munyoki Kilyungi | |
| 2025-09-19 | Remove custom redis service. | Munyoki Kilyungi | |
| 2025-09-19 | Select virtuoso from "gnu". | Munyoki Kilyungi | |
| 2025-09-19 | Explicitly write to "#$repositories" for all the different projects. | Munyoki Kilyungi | |
| 2025-09-19 | Explicitly define a "repositories" dir for cloning gn-projects. | Munyoki Kilyungi | |
| 2025-09-19 | genenetwork-development: Import nss-certs from (gnu packages nss). | Munyoki Kilyungi | |
| 2025-09-03 | Remove hard-coded paths. | Munyoki Kilyungi | |
| 2025-08-16 | virtuoso-ose: patch in a temporary fix. | Frederick Muriuki Muriithi | |
| 2025-08-16 | Add GN_GUILE_SERVER_URL | Munyoki Kilyungi | |
| 2025-08-16 | genenetwork-development: Add gn-guile forge-project. | Munyoki Kilyungi | |
| * genenetwork-development.scm (genenetwork-projects): Add gn-guile. | |||
| 2025-08-16 | genenetwork-development: Add missing guile port. | Munyoki Kilyungi | |
| * genenetwork-development.scm (genenetwork-shepherd-services): Add gn-guile-port. | |||
| 2025-08-16 | genenetwork-development: Add gn-guile to sudoers file. | Munyoki Kilyungi | |
| * genenetwork-development.scm (operating-sytem) [sudoers-file]: Add gn-guile. | |||
| 2025-08-16 | genenetwork-development: <genenetwork-configuration>: New field. | Munyoki Kilyungi | |
| * genenetwork-development.scm (<genenetwork-configuration>) [gn-guile-repository]: New field. | |||
| 2025-08-16 | genenetwork-development: Run gn-guile from gn-guile git path. | Munyoki Kilyungi | |
| 2025-08-11 | Publish channel as either 'gn-bioinformatics or 'guix-bioinformatics | Frederick Muriuki Muriithi | |
| * Either name is acceptable. | |||
| 2025-08-11 | Revert "virtuoso-ose: patch in a temporary fix." | Frederick Muriuki Muriithi | |
| This reverts commit 6402ef859d0057ef4fa9b369dc26719a4c1def9f. | |||
| 2025-08-07 | virtuoso-ose: patch in a temporary fix. | Frederick Muriuki Muriithi | |
| 2025-08-07 | Provide missing config variable. | Frederick Muriuki Muriithi | |
| 2025-07-22 | Override redis with a custom-redis that's not dependent on syslogd. | Munyoki Kilyungi | |
| 2025-07-22 | Set path for lmdb. | Munyoki Kilyungi | |
| We currently use lmdb for storing genotype files. | |||
| 2025-07-22 | Add curl and coreutil-minimal to %base-packages. | Munyoki Kilyungi | |
| This helps when troubleshooting issues from inside the dev container. | |||
| 2025-07-22 | genenetwork-development: Set the profile and ssl-certs inside gexp. | Munyoki Kilyungi | |
| 2025-07-22 | genenetwork-development: Set utf-8 chars in mysql socket. | Munyoki Kilyungi | |
| 2025-07-22 | genenetwork-development: Set "TEST_FEATURE_SWITCH=True". | Munyoki Kilyungi | |
| 2025-07-21 | gn-libs: Use HTTP(s) URI rather than local file paths | Frederick 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. | |||
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