Configuration Reference

This page is a searchable lookup table for BIOMERO Python client configuration. It focuses on options read by SlurmClient.from_config() and their runtime impact.

Resolution And Precedence

For the settings on this page, BIOMERO resolves values in this order:

built-in defaults
values from slurm-config.ini
environment variable overrides, when supported

For sacct history settings, relative-day settings override absolute-date settings.

Use this page as the quick lookup companion to SLURM Configuration Guide, which explains when and why you would choose each setting.

Environment Variable Lookup Table

Supported configuration env vars
Environment variable	`slurm-config.ini` key	Type	Runtime effect
`BIOMERO_SACCT_START_TIME`	`sacct_start_time`	string date	Absolute default start date for job history queries via `sacct`
`BIOMERO_SACCT_START_DAYS_AGO`	`sacct_days_ago`	integer	Rolling history window in days; overrides absolute start time when valid
`BIOMERO_ENV_FILE_SUBMISSION`	`env_file_submission`	boolean	Switches submission from direct env passing to per-job env-file submission
`BIOMERO_INJECT_GPU_FLAG`	`inject_gpu_flag`	boolean	Enables dynamic GPU flag handling in generated scripts and GPU-aware submissions
`BIOMERO_GPU_PARTITION`	`gpu_partition`	string	Default fallback GPU partition for workflow submissions when GPU mode is requested
`BIOMERO_GPU_GRES`	`gpu_gres`	string	Default fallback `--gres=` value appended to GPU workflow submissions; mutually exclusive with `gpu_gpus`
`BIOMERO_GPU_GPUS`	`gpu_gpus`	string	Default fallback `--gpus=` value appended to GPU workflow submissions; mutually exclusive with `gpu_gres`
`BIOMERO_IMAGE_PULL_VIA_SBATCH`	`slurm_image_pull_via_sbatch`	boolean	Switches workflow/converter image pulls from direct remote execution to sbatch jobs
`BIOMERO_PULL_CPUS`	`image_pull_cpus`	string	CPU request used for sbatch-based image pull/build jobs
`BIOMERO_PULL_MEM`	`image_pull_mem`	string	Memory request used for sbatch-based image pull/build jobs
`BIOMERO_APPTAINER_TMPDIR`	`apptainer_tmpdir`	string	Tmp directory exported for Apptainer/Singularity image pull/build commands
`BIOMERO_APPTAINER_CACHEDIR`	`apptainer_cachedir`	string	Cache directory exported for Apptainer/Singularity image pull/build commands
`BIOMERO_SLURM_ZIP_CMD`	`slurm_zip_cmd`	string	Overrides the zip command used on the cluster for packaging results
`BIOMERO_ANALYTICS_REBUILD_START_TIME`	`analytics_rebuild_start_time`	string date	Absolute cutoff date (`YYYY-MM-DD`) from which events are replayed when resetting analytics view tables; leave unset to replay all events
`BIOMERO_ANALYTICS_REBUILD_DAYS_AGO`	`analytics_rebuild_days_ago`	integer	Rolling cutoff window in days for analytics view table rebuilds; overrides the absolute date when set
`GPU_PARTITION`	`gpu_partition`	string	Legacy fallback env var for GPU partition; lower priority than `BIOMERO_GPU_PARTITION`
`GPU_GRES`	`gpu_gres`	string	Legacy fallback env var for GPU gres; lower priority than `BIOMERO_GPU_GRES`
`GPU_GPUS`	`gpu_gpus`	string	Legacy fallback env var for GPU gpus; lower priority than `BIOMERO_GPU_GPUS`

`slurm-config.ini` Lookup Table

Key `[SLURM]` options
Key	Type	Default	Effect
`slurm_data_path`	string	`my-scratch/data`	Base path for transferred workflow data on the cluster
`slurm_images_path`	string	`my-scratch/singularity_images/workflows`	Base path for workflow containers on the cluster
`slurm_converters_path`	string	`my-scratch/singularity_images/converters`	Base path for converter containers on the cluster
`slurm_script_path`	string	`slurm-scripts`	Base path for generated or cloned job scripts
`slurm_script_repo`	string or empty	empty	If set, BIOMERO clones and updates job scripts from this repository instead of generating scripts locally; use with caution, because external script repos can drift out of sync with newer BIOMERO releases and are not the recommended default
`slurm_data_bind_path`	string or empty	unset	Injects `APPTAINER_BINDPATH` into job environments
`slurm_conversion_partition`	string or empty	unset	Partition for data conversion jobs; injected as a real `--partition` flag on the conversion sbatch (and exported as `CONVERSION_PARTITION`). Takes precedence over `slurm_default_partition` for conversion jobs
`slurm_default_partition`	string or empty	unset	Generic fallback `--partition` appended to workflow and conversion jobs that do not already set a partition; per-workflow params, the GPU partition, and `slurm_conversion_partition` take precedence. Overridable via `BIOMERO_DEFAULT_PARTITION`
`sacct_start_time`	string date or empty	`2023-01-01`	Absolute start date used when listing historical jobs
`sacct_days_ago`	integer or empty	unset	Relative history window; takes precedence over `sacct_start_time`
`env_file_submission`	boolean	`false`	Uses env-file based submission instead of direct environment propagation
`inject_gpu_flag`	boolean	`false`	Enables dynamic GPU submission support in generated scripts
`gpu_partition`	string or empty	unset	Shared fallback partition appended for GPU workflow runs when needed
`gpu_gres`	string or empty	unset	Shared fallback `--gres=` value appended for GPU workflow runs; mutually exclusive with `gpu_gpus`
`gpu_gpus`	string or empty	unset	Shared fallback `--gpus=` value appended for GPU workflow runs; mutually exclusive with `gpu_gres`
`sbatch_<key>`	string or empty	unset	Any `[SLURM]` key starting with `sbatch_` adds `--<key>=<value>` to every workflow and conversion submission; per-workflow sbatch overrides (and `slurm_conversion_partition` for the conversion `--partition`) always take precedence
`slurm_image_pull_via_sbatch`	boolean	`false`	Uses sbatch jobs instead of direct remote execution for workflow/converter image pulls
`image_pull_cpus`	string	`8`	CPU request for sbatch-based image pull/build jobs
`image_pull_mem`	string	`32G`	Memory request for sbatch-based image pull/build jobs
`apptainer_tmpdir`	string or empty	unset	Tmp directory exported for Apptainer/Singularity image pull/build commands
`apptainer_cachedir`	string or empty	unset	Cache directory exported for Apptainer/Singularity image pull/build commands
`slurm_zip_cmd`	string or empty	`$(command -v 7z \|\| command -v 7za)`	Command used for result zipping on the HPC
`analytics_rebuild_start_time`	string date or empty	unset	Absolute cutoff date (`YYYY-MM-DD`) from which events are replayed when resetting analytics view tables; leave unset to replay all events. Configured under `[ANALYTICS]`.
`analytics_rebuild_days_ago`	integer or empty	unset	Rolling cutoff window in days for analytics view table rebuilds; overrides the absolute date when set. Configured under `[ANALYTICS]`.
`<name>_use_gpu`	boolean	`false`	Per-workflow GPU default in `[WORKFLOWS]` (or `[MODELS]` for legacy configs); e.g. `cellpose_use_gpu=true` marks a workflow as GPU-enabled so BIOMERO activates GPU handling without requiring an explicit `use_gpu` argument at submission time
`<name>_repo`	string URL	—	GitHub URL for a workflow in `[WORKFLOWS]` (or `[MODELS]`). Accepts either a repository tree URL (`…/tree/vX.Y.Z`) or a direct URL to a specific descriptor file (`…/tree/vX.Y.Z/descriptor.json`, `…/tree/vX.Y.Z/config.yaml`). With a plain tree URL, BIOMERO auto-discovers the descriptor (tries `descriptor.json` → `descriptor.yaml` → `config.yaml` in order). With a direct URL, only that exact file is fetched — useful when a repository contains both a BIAflows `descriptor.json` and a bilayers `config.yaml` and you want to choose which interface to expose.

Behaviour Notes

Boolean parsing

Supported truthy values are:

true
1
yes
y
on

Supported falsy values are:

false
0
no
n
off

Invalid boolean env var values fall back to the already resolved ini or default value.

Integer parsing

Invalid integer env var values also fall back to the already resolved ini or default value. This matters especially for BIOMERO_SACCT_START_DAYS_AGO.

Empty-string handling

Some optional string settings treat an empty value as unset rather than as a literal empty string. This is relevant for values such as slurm_data_bind_path, slurm_conversion_partition, slurm_default_partition, gpu_partition, gpu_gres, gpu_gpus, and the optional sacct window settings.

GPU precedence

For workflow submissions, GPU-related settings are applied in this order:

per-workflow sbatch parameters from [WORKFLOWS] (or [MODELS]) such as cellpose_job_partition, cellpose_job_gres, and cellpose_job_gpus
global sbatch defaults from sbatch_<key> entries in [SLURM]
shared runtime GPU defaults: gpu_partition and either gpu_gres (--gres=) or gpu_gpus (--gpus=); these two are mutually exclusive — set one or the other, never both
no BIOMERO-added GPU resource arguments

Shared GPU defaults (level 3) are considered when GPU mode is active. GPU mode is activated by one of two code paths:

Dynamic path (inject_gpu_flag=true): use_gpu is resolved at submission time — explicit use_gpu argument wins, otherwise falls back to <name>_use_gpu from [WORKFLOWS]/[MODELS]. GPU_FLAG env var is set (--nv or empty) at submission time so the script can toggle the container runtime flag.
Static path (inject_gpu_flag=false): --nv is baked into the generated script at script-generation time; only <name>_use_gpu=true in [WORKFLOWS]/[MODELS] triggers GPU sbatch resource param injection, and it cannot be overridden at submission time. No GPU_FLAG env var is set.

See SLURM Configuration Guide for a full explanation of the interaction between these settings.

Search Hints

If you are looking for a specific name, try searching the docs for any of these exact identifiers:

BIOMERO_SACCT_START_TIME
BIOMERO_SACCT_START_DAYS_AGO
BIOMERO_ENV_FILE_SUBMISSION
BIOMERO_INJECT_GPU_FLAG
BIOMERO_GPU_PARTITION
BIOMERO_GPU_GRES
BIOMERO_GPU_GPUS
BIOMERO_IMAGE_PULL_VIA_SBATCH
BIOMERO_PULL_CPUS
BIOMERO_PULL_MEM
BIOMERO_APPTAINER_TMPDIR
BIOMERO_APPTAINER_CACHEDIR
BIOMERO_SLURM_ZIP_CMD
BIOMERO_ANALYTICS_REBUILD_START_TIME
BIOMERO_ANALYTICS_REBUILD_DAYS_AGO
GPU_PARTITION
GPU_GRES
GPU_GPUS