omnibenchmark workflow

Powered by Snakemake

How to

make install to install dependencies
make activate to activate the environment with the dependencies (pipenv shell)
make benchmark to run the benchmark (= trigger the Snakefile)
make dry to dry run the benchmark (= dry run the Snakefile)
make clean deletes the ./out and ./log output folders

Parse a YAML specification of a benchmark and dynamically build snakemake rules to build the suitable workflow.

Develop in branch dev, seldom merged to main

05 Feb 2024, Izaskun Mallona

Name	Name	Last commit message	Last commit date
Latest commit DanInci Merge pull request #10 from omnibenchmark/run_module Jul 30, 2024 9ef84c8 · Jul 30, 2024 History 81 Commits
data	data	Update module references for Benchmark_001.yaml	Jul 16, 2024
src	src	Include benchmark information in serialized Snakefile	Jul 22, 2024
.gitignore	.gitignore	Add some more inferred types and documentation to workflow engine	Jun 11, 2024
LICENSE	LICENSE	Initial commit	Jan 16, 2024
Makefile	Makefile	Module execution: clone repository, checkout commit, execute run.sh	Jun 27, 2024
Pipfile	Pipfile	Module execution: clone repository, checkout commit, execute run.sh	Jun 27, 2024
README.md	README.md	Untested/dirty end of the week commit	Feb 23, 2024
main.py	main.py	Some refactoring + include Almut's stage_order code	Jul 22, 2024