add conda environment file and minimal CI

dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

MIT License

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add conda environment file and minimal CI #113

Closed lkeegan closed 1 year ago

lkeegan commented 2 years ago

add environment.yml
- a conda environment with all required dependencies (on linux)
- external dependencies from documentation flexbar/bowtie2/star/samtools are installed from bioconda
- dependencies from requirements.txt are installed using pip
add github actions workflow CI
- installs the conda environment
- installs rp-bp
- downloads the test data
- runs the examples from the documentation
- linux only for now (flexbar not available for mac on bioconda)

lkeegan commented 2 years ago

CI output: https://github.com/lkeegan/rp-bp/runs/7109075224?check_suite_focus=true

eboileau commented 1 year ago

This PR was added to a new branch dev-ssciwr. We can work on this branch. The minimal CI runs fine. Next steps: actually implement the tests, also check linux only for now (flexbar not available for mac on bioconda).