BIOMERO
BIOMERO - Get Started
BIOMERO - BioImage analysis in OMERO
Overview
Quickstart
Prerequisites & Getting Started with BIOMERO
BIOMERO scripts
(Docker) containers
See the tutorials
SSH
SlurmClient class
slurm-config.ini
How to add an existing workflow
How to add your new custom workflow
Slurm jobs
Batching
Using the GPU on Slurm
Transfering data
Testing the Python code
Logging
Tutorials
Cellprofiler tutorial
CellExpansion tutorial
Local Slurm tutorial
Google Cloud Slurm tutorial
Microsoft Azure Slurm tutorial
Extra thoughts
Package
biomero
BIOMERO
Index
Index
B
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C
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E
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F
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G
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I
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J
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L
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M
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O
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P
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R
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S
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T
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U
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V
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W
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Z
B
biomero.slurm_client
module
C
check_job_status() (biomero.slurm_client.SlurmClient method)
cleanup() (biomero.slurm_client.SlurmJob method)
cleanup_tmp_files() (biomero.slurm_client.SlurmClient method)
completed() (biomero.slurm_client.SlurmJob method)
convert_cytype_to_omtype() (biomero.slurm_client.SlurmClient method)
convert_url() (biomero.slurm_client.SlurmClient method)
copy_zip_locally() (biomero.slurm_client.SlurmClient method)
E
error_message (biomero.slurm_client.SlurmJob attribute)
extract_data_location_from_log() (biomero.slurm_client.SlurmClient method)
extract_job_id() (biomero.slurm_client.SlurmClient method)
extract_parts_from_url() (biomero.slurm_client.SlurmClient method)
F
from_config() (biomero.slurm_client.SlurmClient class method)
G
generate_slurm_job_for_workflow() (biomero.slurm_client.SlurmClient method)
get_active_job_progress() (biomero.slurm_client.SlurmClient method)
get_all_image_versions_and_data_files() (biomero.slurm_client.SlurmClient method)
get_cellpose_command() (biomero.slurm_client.SlurmClient method)
get_conversion_command() (biomero.slurm_client.SlurmClient method)
get_error() (biomero.slurm_client.SlurmJob method)
get_image_versions_and_data_files() (biomero.slurm_client.SlurmClient method)
get_job_status_command() (biomero.slurm_client.SlurmClient method)
get_jobs_info_command() (biomero.slurm_client.SlurmClient method)
get_logfile_from_slurm() (biomero.slurm_client.SlurmClient method)
get_or_create_github_session() (biomero.slurm_client.SlurmClient method)
get_recent_log_command() (biomero.slurm_client.SlurmClient method)
get_unzip_command() (biomero.slurm_client.SlurmClient method)
get_update_slurm_scripts_command() (biomero.slurm_client.SlurmClient method)
get_workflow_command() (biomero.slurm_client.SlurmClient method)
get_workflow_parameters() (biomero.slurm_client.SlurmClient method)
get_zip_command() (biomero.slurm_client.SlurmClient method)
I
init_workflows() (biomero.slurm_client.SlurmClient method)
J
job_id (biomero.slurm_client.SlurmJob attribute)
job_state (biomero.slurm_client.SlurmJob attribute)
L
list_active_jobs() (biomero.slurm_client.SlurmClient method)
list_all_jobs() (biomero.slurm_client.SlurmClient method)
list_available_converter_versions() (biomero.slurm_client.SlurmClient method)
list_completed_jobs() (biomero.slurm_client.SlurmClient method)
M
module
biomero.slurm_client
O
ok (biomero.slurm_client.SlurmJob attribute)
P
parse_docker_image_version() (biomero.slurm_client.SlurmClient method)
pull_descriptor_from_github() (biomero.slurm_client.SlurmClient method)
R
run_commands() (biomero.slurm_client.SlurmClient method)
run_commands_split_out() (biomero.slurm_client.SlurmClient method)
run_conversion_workflow_job() (biomero.slurm_client.SlurmClient method)
run_workflow() (biomero.slurm_client.SlurmClient method)
run_workflow_job() (biomero.slurm_client.SlurmClient method)
S
setup_container_images() (biomero.slurm_client.SlurmClient method)
setup_converters() (biomero.slurm_client.SlurmClient method)
setup_directories() (biomero.slurm_client.SlurmClient method)
setup_job_scripts() (biomero.slurm_client.SlurmClient method)
setup_slurm() (biomero.slurm_client.SlurmClient method)
slurm_converters_path (biomero.slurm_client.SlurmClient attribute)
slurm_data_path (biomero.slurm_client.SlurmClient attribute)
slurm_images_path (biomero.slurm_client.SlurmClient attribute)
slurm_model_images (biomero.slurm_client.SlurmClient attribute)
slurm_model_paths (biomero.slurm_client.SlurmClient attribute)
slurm_model_repos (biomero.slurm_client.SlurmClient attribute)
slurm_script_path (biomero.slurm_client.SlurmClient attribute)
slurm_script_repo (biomero.slurm_client.SlurmClient attribute)
SlurmClient (class in biomero.slurm_client)
SlurmJob (class in biomero.slurm_client)
str_to_class() (biomero.slurm_client.SlurmClient method)
submit_result (biomero.slurm_client.SlurmJob attribute)
T
transfer_data() (biomero.slurm_client.SlurmClient method)
U
unpack_data() (biomero.slurm_client.SlurmClient method)
update_slurm_scripts() (biomero.slurm_client.SlurmClient method)
V
validate() (biomero.slurm_client.SlurmClient method)
W
wait_for_completion() (biomero.slurm_client.SlurmJob method)
workflow_params_to_envvars() (biomero.slurm_client.SlurmClient method)
workflow_params_to_subs() (biomero.slurm_client.SlurmClient method)
Z
zip_data_on_slurm_server() (biomero.slurm_client.SlurmClient method)