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slurm-config.ini
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[SSH]
# -------------------------------------
# SSH settings
# -------------------------------------
# The alias for the SLURM SSH connection
host=slurm
# Set the rest of your SSH configuration in your SSH config under this host name/alias
# Or in e.g. /etc/fabric.yml (see Fabric's documentation for details on config loading)
[SLURM]
# -------------------------------------
# Slurm settings
# -------------------------------------
# General settings for where to find things on the Slurm cluster.
# -------------------------------------
# PATHS
# -------------------------------------
# The path on SLURM entrypoint for storing datafiles
#
# Note:
# This example is relative to the Slurm user's home dir
slurm_data_path=my-scratch/data
# The path on SLURM entrypoint for storing container image files
#
# Note:
# This example is relative to the Slurm user's home dir
slurm_images_path=my-scratch/singularity_images/workflows
# The path on SLURM entrypoint for storing converter image files
#
# Note:
# This example is relative to the Slurm user's home dir
slurm_converters_path=my-scratch/singularity_images/converters
# The path on SLURM entrypoint for storing the slurm job scripts
#
# Note:
# This example is relative to the Slurm user's home dir
slurm_script_path=my-scratch/slurm-scripts
# -------------------------------------
# REPOSITORIES
# -------------------------------------
# A (github) repository to pull the slurm scripts from.
#
# Note:
# If you provide no repository, we will generate scripts instead!
# Based on the job_template.sh and the descriptor.json
#
# Example:
#slurm_script_repo=https://github.com/TorecLuik/slurm-scripts
slurm_script_repo=
# -------------------------------------
# Processing settings
# -------------------------------------
# General/default settings for processing jobs.
# Note: NOT YET IMPLEMENTED
# Note: If you need to change it for a specific case only,
# you should change the job script instead, either in OMERO or Slurm
[CONVERTERS]
# -------------------------------------
# Converters settings
# -------------------------------------
# Settings for linking to external converters.
#
# By default, BIOMERO exports images as ZARR to the HPC.
# But, the workflow you want to execute might require
# a different filetype. E.g. most of our example workflows
# require TIFF input files.
#
# By default we will build a converter on Slurm for you.
# Theoretically you can add other converters here to pull
# those instead. These should be available on dockerhub.
#
# -------------------------------------
# ZARR TO TIFF
# -------------------------------------
# Uncomment this if you want to pull the image instead of
# build it. E.g. if you don't have singularity build rights
# on your Slurm.
#
# Please pin it to a specific version to reduce unforeseen errors.
#
# Key should be the types "X_to_Y" and value should be the docker image
#zarr_to_tiff=cellularimagingcf/convert_zarr_to_tiff:1.14.0
[MODELS]
# -------------------------------------
# Model settings
# -------------------------------------
# Settings for models/singularity images that we want to run on Slurm
#
# NOTE: keys have to be unique, and require a <key>_repo and <key>_image value as well.
#
# NOTE 2: Versions for the repo are highly encouraged!
# Latest/master can change and cause issues with reproducability!
# We pickup the container version based on the version of the repository.
# For generic master branch, we pick up generic latest container.
# -------------------------------------
# CELLPOSE SEGMENTATION
# -------------------------------------
# The path to store the container on the slurm_images_path
cellpose=cellpose
# The (e.g. github) repository with the descriptor.json file
cellpose_repo=https://github.com/TorecLuik/W_NucleiSegmentation-Cellpose/tree/v1.2.7
# The jobscript in the 'slurm_script_repo'
cellpose_job=jobs/cellpose.sh
# Override the default job values for this workflow
# Or add a job value to this workflow
# For more examples of such parameters, google SBATCH parameters.
# If you don't want to override, comment out / delete the line.
# Run CellPose Slurm with 10 GB GPU
cellpose_job_gres=gpu:1g.10gb:1
# e.g. Run on a different partition
# cellpose_job_partition=partition_with_gpu
# -------------------------------------
# STARDIST SEGMENTATION
# -------------------------------------
# The path to store the container on the slurm_images_path
stardist=stardist
# The (e.g. github) repository with the descriptor.json file
stardist_repo=https://github.com/Neubias-WG5/W_NucleiSegmentation-Stardist/tree/v1.3.2
# The jobscript in the 'slurm_script_repo'
stardist_job=jobs/stardist.sh
# -------------------------------------
# CELLPROFILER SEGMENTATION
# -------------------------------------
# The path to store the container on the slurm_images_path
cellprofiler=cellprofiler
# The (e.g. github) repository with the descriptor.json file
cellprofiler_repo=https://github.com/Neubias-WG5/W_NucleiSegmentation-CellProfiler/tree/v1.6.4
# The jobscript in the 'slurm_script_repo'
cellprofiler_job=jobs/cellprofiler.sh
# -------------------------------------
# DEEPCELL SEGMENTATION
# -------------------------------------
# The path to store the container on the slurm_images_path
deepcell=deepcell
# The (e.g. github) repository with the descriptor.json file
deepcell_repo=https://github.com/Neubias-WG5/W_NucleiSegmentation-DeepCell/tree/v.1.4.3
# The jobscript in the 'slurm_script_repo'
deepcell_job=jobs/deepcell.sh
# -------------------------------------
# IMAGEJ SEGMENTATION
# -------------------------------------
# The path to store the container on the slurm_images_path
imagej=imagej
# The (e.g. github) repository with the descriptor.json file
imagej_repo=https://github.com/Neubias-WG5/W_NucleiSegmentation-ImageJ/tree/v1.12.10
# The jobscript in the 'slurm_script_repo'
imagej_job=jobs/imagej.sh
# -------------------------------------
# CELLPROFILER SPOT COUNTING
# -------------------------------------
# The path to store the container on the slurm_images_path
cellprofiler_spot=cellprofiler_spot
# The (e.g. github) repository with the descriptor.json file
cellprofiler_spot_repo=https://github.com/TorecLuik/W_SpotCounting-CellProfiler/tree/v1.0.1
# The jobscript in the 'slurm_script_repo'
cellprofiler_spot_job=jobs/cellprofiler_spot.sh
# -------------------------------------
# CELLEXPANSION SPOT COUNTING
# -------------------------------------
# The path to store the container on the slurm_images_path
cellexpansion=cellexpansion
# The (e.g. github) repository with the descriptor.json file
cellexpansion_repo=https://github.com/TorecLuik/W_CellExpansion/tree/v1.0.1
# The jobscript in the 'slurm_script_repo'
cellexpansion_job=jobs/cellexpansion.sh
# -------------------------------------
# MEASUREMENTS - 2 masks (cell + nucleus)
# -------------------------------------
# The path to store the container on the slurm_images_path
nuclei_measurements=nuclei_measurements
# The (e.g. github) repository with the descriptor.json file
nuclei_measurements_repo=https://github.com/Cellular-Imaging-Amsterdam-UMC/W_Measurements-Nuclei-CellProfiler/tree/v1.0.0
# The jobscript in the 'slurm_script_repo'
nuclei_measurements_job=jobs/nuclei_measurements.sh
# Run Slurm with more GB CPU memory
# nuclei_measurements_job_mem=32GB
# Run Slurm with higher timeout value (d-hh:mm:ss)
# nuclei_measurements_job_time=01:00:00
# -------------------------------------
# MEASUREMENTS - 3 masks (cell + nucleus + aggregate)
# -------------------------------------
# The path to store the container on the slurm_images_path
aggregates_measurements=aggregates_measurements
# The (e.g. github) repository with the descriptor.json file
aggregates_measurements_repo=https://github.com/Cellular-Imaging-Amsterdam-UMC/W_Measurements-CellProfiler/tree/v1.1.0
# The jobscript in the 'slurm_script_repo'
aggregates_measurements_job=jobs/aggregates_measurements.sh
# Run Slurm with more GB CPU memory
# aggregates_measurements_job_mem=32GB
# Run Slurm with higher timeout value (d-hh:mm:ss)
# aggregates_measurements_job_time=01:00:00