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* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set REAPER_COMMAND in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Set GENOTYPE_FILES in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork-development.scm (set-build-directory-permissions-gexp):
New variable.
* genenetwork-development.scm (operating-system)[services]: Use
set-build-directory-permissions-gexp.
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* genenetwork-development.scm (gn-gemtext-threads-project)[ci-jobs]:
Set LC_ALL environment variable.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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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"
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* slurm.scm (slurm): Upgrade to 24.05.3.
[arguments]: Remove Unix socket disabling.
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* slurm.scm (slurm)[arguments]: Add --with-yaml configure flag.
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* slurm-worker-deploy.sh: Install slurmrestd too.
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* slurm-deploy.sh: Delete file.
* slurm-head-deploy.sh, slurm-worker-deploy.sh: New files.
* slurm.scm: Replace tux04 with octopus in comment.
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* slurm.scm: Import http-parser from (gnu packages web).
(http-parser): Delete variable.
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Fix the service activation code to make the gn-uploader data
directory, and all its children belong to the app user.
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Make the container's logs available of the host to help with
troubleshooting and some stickiness for the logs.
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While it is a tiny change, it does help to have an explicit indication
of what container you are currently working with, especially when you
need to do specific tasks inside the container itself with something
like `nsenter …` or `guix container exec …`.
With this commit, instead of a generic prompt like:
`root@genenetwork /#`,
you get a more specific prompt such as
`root@genenetwork-production /#`
which goes some ways in avoiding mistakes.
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Add the scheduled indexer service to the
genenetwork-service-type. This will run the indexer script every hour.
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Pass in the configuration to the gexp building function to make the
builder function work across environments.
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* slurm-deploy.sh, slurm.scm: New files.
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Directories need the execute bit set to actually be accessible to the
owner.
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Put the secrets for the different services in service-specific
directories, all of them sharing the same parent directory.
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* genenetwork-development.scm: Run "M-x untabify".
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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>
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* genenetwork-development.scm (guile-lapack-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lapack-project.
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* genenetwork-development.scm (guile-gsl-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-gsl-project.
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The profile path is necessary for use retrieving the included
bootstrap content.
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* genenetwork/services/genenetwork.scm: Import nginx from (gnu
packages web), python from (gnu packages python), (guix build
python-build-system) and (guix packages).
(gn-uploader-nginx-server-block): Serve static files via nginx.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* genenetwork-development.scm (genenetwork-shepherd-services): Mount
llm-db-path into genenetwork3 container.
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genenetwork-development.scm (<genenetwork-configuration>)[llm-db-path]:
New field.
(genenetwork3-cd-gexp): Configure LLM_DB_PATH in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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