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2023-11-02gn-auth: Remove automated migrations.Frederick Muriuki Muriithi
2023-10-28Do not use upstream Guix in CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Remove default upstream Guix channels.
2023-10-05Fix guix-bioinformatics path in project definition.Arun Isaac
* genenetwork-development.scm (guix-bioinformatics-project)[repository]: Fix path.
2023-10-05Fix typo in comment about cloning the latest gn-auth repository.Arun Isaac
* genenetwork-development.scm (gn-auth-migrations-laminar): Fix typo in comment.
2023-10-05Construct yoyo.ini using guile-ini.Arun Isaac
Constructing INI files from S-expressions instead of using string substitutions is a little nicer. * genenetwork-development.scm (gn-auth-migrations-yoyo-ini-gexp): New function. (gn-auth-migrations): Use gn-auth-migrations-yoyo-ini-gexp.
2023-10-05Mount git repositories read-write.Arun Isaac
* genenetwork-development-deploy.sh: Mount /home/git/public read-write into the container.
2023-10-04Use guix-bioinformatics repository on tux02.Arun Isaac
The guix-bioinformatics repository is now on tux02. There is no webhook to listen for. So, use it directly as a local repository. * genenetwork-development.scm (guix-bioinformatics-project)[repository]: Use local repository on tux02.
2023-10-04Import gn-auth from (gn packages genenetwork).Arun Isaac
* genenetwork-development.scm: Import gn-auth from (gn packages genenetwork) instead of from (gn-auth) or elsewhere.
2023-10-04Import python-mypy from (gnu packages python).Arun Isaac
* genenetwork-development.scm: Import python-mypy from (gnu packages python) instead of (gn packages python).
2023-10-04Use switch-symlinks from (guix build utils).Arun Isaac
switch-symlinks was recently moved from (guix utils) to (guix build utils). It can now be safely used in build-side code. * genenetwork-development.scm (install-laminar-template-gexp): Use switch-symlinks from (guix build utils).
2023-09-28Use upstream mypy.Munyoki Kilyungi
* genenetwork-development.scm: Replace python-mypy-0.981 import with upstream version. (genenetwork3-mypy, genenetwork-projects): Replace python-mypy-0.981 with upstream version. Acked-by: Arun Isaac <arunisaac@systemreboot.net>
2023-09-27Revert "Set the envvar in the gexp"Frederick Muriuki Muriithi
This reverts commit 416bf833737b23e86756b68e0cb162529bbd2665.
2023-09-27Revert "Expose configurations directory to pola-wrapper."Frederick Muriuki Muriithi
This reverts commit 5ec4b45702cba430b8da47949f37317527cf05a6.
2023-09-27Revert "Expose config file to pola-wrapper"Frederick Muriuki Muriithi
This reverts commit d12e7e45883df361ab4f78055c8112ded2e896ca.
2023-09-20Expose config file to pola-wrapperFrederick Muriuki Muriithi
2023-09-20Expose configurations directory to pola-wrapper.Frederick Muriuki Muriithi
2023-09-20Set the envvar in the gexpFrederick Muriuki Muriithi
2023-09-20Pass "secrets" configurations to GN2Frederick Muriuki Muriithi
We need to pass in secrets to the running applications. This commit does it for GeneNetwork2.
2023-09-19Use appropriate mypy for Python3.10Frederick Muriuki Muriithi
2023-09-19Add missing `gn-auth-repository` configurationFrederick Muriuki Muriithi
2023-09-16Add CI/CD definitions for gn-authFrederick Muriuki Muriithi
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Update the repo-url for transforming genenetwork databases.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use correct name for python-mypyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Update arguments to pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use mypy defined in guix-bioinformaticsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-04Use self-hosted git repoMunyoki Kilyungi
2023-09-04Use self-hosted GN repositoryMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-12Add link to git repoPjotr Prins
2023-08-10Set up cgit service.Arun Isaac
* genenetwork-development.scm: Import (forge cgit). (operating-system)[services]: Add cgit service. * genenetwork-development-deploy.sh: Expose cgit repository directory.
2023-08-10Switch to the forge-nginx and ACME services.Arun Isaac
* genenetwork-development.scm: Import only nginx-server-configuration and nginx-location-configuration from (gnu services web). Import (forge acme) and (forge nginx). (development-server-reverse-proxy-server-block, laminar-reverse-proxy-server-block, tissue-reverse-proxy-server-block): Remove listen argument. (operating-system)[sudoers-file]: Permit the acme user to restart nginx. [services]: Replace nginx service with a forge-nginx service. Add ACME service. * genenetwork-development-deploy.sh: Share /var/lib/acme.
2023-08-10Add nginx package with the ssl_preread module.Arun Isaac
* nginx-preread.scm, nginx-preread-deploy.sh: New files.
2023-07-27README: Remove references to penguin2.Arun Isaac
penguin2 is no more. We now use tux02 for development. * README.org: Change references to penguin2 to tux02.
2023-07-27Revert "README: host names"Arun Isaac
This reverts commit fc65c2a2c056ee9f313631da6e5f93adec277dd5.
2023-07-19Use tissue from guix-forge.Arun Isaac
The libgit2 patch is now in guix-forge. So, we don't have to repeat it here. * genenetwork-development.scm (libgit2-1.3, guile-git-for-tissue, tissue): Delete variables. (operating-system)[services]: Do not specify package for tissue service.
2023-07-19Disable verbose build logs for guix-bioinformatics job.Arun Isaac
* genenetwork-development.scm (guix-bioinformatics-project): Disable verbose build logs.
2023-07-19Use guix-channel-job-gexp for genenetwork3 tests.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Use guix-channel-job-gexp for genenetwork3 tests.
2023-07-19Add guix-bioinformatics CI job.Arun Isaac
* genenetwork-development.scm (guix-channel-job-gexp): New function. (guix-bioinformatics-project): New variable. (operating-system)[services]: Add guix-bioinformatics-project to forge-service-type.
2023-07-11README: host namesPjotr Prins
2023-07-11Revert "Disable tests"Munyoki Kilyungi
This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
2023-07-10Add a troubleshooting subsection to READMEMunyoki Kilyungi
2023-07-10Revert "Fix genotype file path"Munyoki Kilyungi
This reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.
2023-07-10Fix genotype file pathMunyoki Kilyungi
2023-07-10Disable testsMunyoki Kilyungi
Rob is giving a demo, so disable tests and fix them later. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-10Basic mail/opensmtpd service addedPjotr Prins
2023-06-26Add virtuoso allowed dirsMunyoki Kilyungi
2023-06-15Increase threshold for number-of-buffers and maximum-dirty-buffers.Munyoki Kilyungi
* genenetwork-development.scm, public-sparql.scm (operating-system)[services]<virtuoso-service>: Set number-of-buffers and maximum-dirty-buffers. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-15Add links to README.Munyoki Kilyungi
* README.org (GeneNetwork development container): Link to guix-bioinformatics and guix-forge channels. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2023-06-08Share auth-db-path with genenetwork3-pola-wrapper.Frederick Muriuki Muriithi
* genenetwork-development.scm (genenetwork-shepherd-services): Share auth-db-path with genenetwork3-pola-wrapper. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 02:51:54 +0000