CLI
Usage:
$ [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
benchmark: Manage benchmarks and their versions.files: List, download and check input/output files.run: Execute benchmarks or modules.software: Manage and install benchmark-specific...
benchmark
Manage benchmarks and their versions.
Usage:
$ benchmark [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
diff: Show differences between 2 benchmark...list-versions: List all available benchmarks versions at...
benchmark diff
Show differences between 2 benchmark versions.
Usage:
$ benchmark diff [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-v1, --version1 TEXT: reference version [required]-v2, --version2 TEXT: version to compare with. [required]--help: Show this message and exit.
benchmark list-versions
List all available benchmarks versions at a specific endpoint.
Usage:
$ benchmark list-versions [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-e, --endpoint TEXT: remote/object storage. [required]--help: Show this message and exit.
files
List, download and check input/output files.
Usage:
$ files [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
download: Download all or specific files for a...list: List all or specific files for a benchmark.
files download
Download all or specific files for a benchmark.
Usage:
$ files download [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-t, --type TEXT: File types. Options: all, code, inputs, outputs, logs, performance. [default: all]-s, --stage TEXT: Stage to download files from.-m, --module TEXT: Module to download files from.-i, --id TEXT: File id to download.--help: Show this message and exit.
files list
List all or specific files for a benchmark.
Usage:
$ files list [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-t, --type TEXT: File types. Options: all, code, inputs, outputs, logs, performance. [default: all]-s, --stage TEXT: Stage to list files for.-m, --module TEXT: Module to list files for.-i, --id TEXT: File id/type to list.--help: Show this message and exit.
run
Execute benchmarks or modules.
Usage:
$ run [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
benchmark: Run a benchmark as specified in the yaml.module: Run a specific module on various datasets...validate: Validate a benchmark yaml.
run benchmark
Run a benchmark as specified in the yaml.
Usage:
$ run benchmark [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-p, --threads INTEGER: The parallelism level for the workflow scheduler. [default: 1]-u, --update: Force re-run execution for all modules and stages.-d, --dry: Dry run-l, --local: Execute and store results locally. Default False.--help: Show this message and exit.
run module
Run a specific module on various datasets or custom inputs. This command does not have a default behavior. You must explicitly choose one of the following options:
--input: Provide a path to a custom directory to use as the input dataset.--example: Set this flag to execute the module on a remote example dataset.--all: Set this flag to run the module on all available remote datasets.
Note: You must select one of these options for the command to run.
Usage:
$ run module [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]-m, --module TEXT: Module (ID) to execute. [required]-i, --input TEXT: Run on inputs from input directory.-e, --example: Run on remote example inputs only.-a, --all: Run on all valid benchmark inputs.-u, --update: Force re-run execution for all modules and stages.-d, --dry: Dry run--help: Show this message and exit.
run validate
Validate a benchmark yaml.
Usage:
$ run validate [OPTIONS]
Options:
-b, --benchmark TEXT: Path to benchmark yaml file or benchmark id. [required]--help: Show this message and exit.
software
Manage and install benchmark-specific software environments
Usage:
$ software [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
check: Check whether the component {what} is...conda: Manage conda-based software installations.envmodules: Manage envmodules-based software...singularity: Manage singularity- (apptainer-) based...
software check
Check whether the component {what} is available.
Usage:
$ software check [OPTIONS]
Options:
-w, --what TEXT: Binary/functionality to check:
--what singularity : singularity
--what module : module tool, typically lmod
--what easybuild : easybuild
--what conda : conda [required]
* --help: Show this message and exit.
software conda
Manage conda-based software installations. Does not use easybuild.
Usage:
$ software conda [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
pin: Pin all conda env-related dependencies...
software conda pin
Pin all conda env-related dependencies versions using snakedeploy.
Usage:
$ software conda pin [OPTIONS]
Options:
-e, --env TEXT: Path to the conda env file. [required]--help: Show this message and exit.
software envmodules
Manage envmodules-based software installations. Uses easybuild to build software.
Usage:
$ software envmodules [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
build: Build a given easyconfig (and generates...
software envmodules build
Build a given easyconfig (and generates the relevant envmodules).
Usage:
$ software envmodules build [OPTIONS]
Options:
-e, --easyconfig TEXT: Easyconfig [required]-p, --threads INTEGER: Number of threads [default: 2]--help: Show this message and exit.
software singularity
Manage singularity- (apptainer-) based software installations. Uses easybuild to build software.
Usage:
$ software singularity [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
build: Build a singularity (fakeroot) image for a...push: Pushes a singularity SIF file to an...
software singularity build
Build a singularity (fakeroot) image for a given easyconfig.
Usage:
$ software singularity build [OPTIONS]
Options:
-e, --easyconfig TEXT: Easyconfig [required]--help: Show this message and exit.
software singularity push
Pushes a singularity SIF file to an ORAS-compatible registry.
Usage:
$ software singularity push [OPTIONS]
Options:
-u, --docker_username TEXT: Docker username [required]-p, --docker_password TEXT: Docker password (token) [required]-s, --sif PATH: Path to the Singularity SIF file [required]-o, --oras TEXT: Registry's ORAS static URL, for instance oras://registry.mygitlab.ch/myuser/myproject:mytag [required]--help: Show this message and exit.