dgenies

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Until now jobs execution paths are different in standalone mode and in server mode and depending if the runner is local or use drmaa It leads to many duplicate code...

pbordron

Create a collection of post-install scripts - Copy static resources to another directory for http proxy (like nginx). At least get the path of files/dirs that can be served statically...

pbordron

Simplify access to maintenance scripts

1

Scripts `dgenies/bin/clean_jobs.py` and `dgenies/bin/local_scheduler.py` are not easily accessible. For example, the full path of `clean_jobs.py` in a virtualenv is the following: ``` /usr/local/venv/dgenies/lib/python3.6/site-packages/dgenies-1.5.0-py3.6.egg/dgenies/bin/clean_jobs.py ``` Possibles solutions: - complete dgenies program...

pbordron

Update computation time related infrastructure evolution, new software versions, etc. #65

pbordron

When running dgenies after an update, migrate database automagically to new schema if needed

pbordron

Packaging

1

Update `setup.py` in order to target many install use cases Until now, doing a `pip install dgenies` install dgenies ready for cluster (with web server dependencies and `drmaa`). We can...

pbordron

Check email with more elaborate regex with - [py3-validate-email](https://pypi.org/project/py3-validate-email), [email-validator](https://pypi.org/project/email-validator) - or [pyIsEmail](https://pypi.org/project/pyIsEmail)

pbordron

Add systemd recipes for - dgenies (gunicorn + nginx proxy) - dgenies-scheduler with timer (instead of cron) - dgenies cleaning with timer (instead of cron) Will use #103 Also add...

pbordron

CD/CI

1

Write ci/cd rules - [ ] Write integration tests (needs #62) - [ ] Packaging - [ ] Publication on `pip` (bioconda will pull with conda-bot, but sometime the recipe...

pbordron

When starting dgenies scheduler, "clean" registred jobs that are not in following state by setting them to failed: - fail - no match - success - waiting - cluster? -...

pbordron