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tieneupintieneupin
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Update CLEM recipes (#177)
* Created copies of the wrapper versions of the CLEM recipes * Modified the main CLEM recipes to use the service instead of the wrapper
1 parent f617210 commit 35d042c

6 files changed

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‎recipes/clem-align-and-merge-wrapper.json‎

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{
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"1": {
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"job_parameters": {
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"series_name": "{series_name}",
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"images": "{images}",
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"metadata": "{metadata}",
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"crop_to_n_frames": "{crop_to_n_frames}",
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"align_self": "{align_self}",
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"flatten": "{flatten}",
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"align_across": "{align_across}"
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},
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMAlignAndMerge -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "align-and-merge",
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"memory_per_node": 65536,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 8,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_align_and_merge--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "ALIGN-AND-MERGE"
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},
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"2": {
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"parameters": {
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"session_id": "{session_id}"
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},
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"queue": "{feedback_queue}",
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"service": "Murfey"
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},
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"start": [[1, []]]
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}

‎recipes/clem-align-and-merge.json‎

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{
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"1": {
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"job_parameters": {
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"parameters": {
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"series_name": "{series_name}",
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"images": "{images}",
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"metadata": "{metadata}",
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMAlignAndMerge -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "align-and-merge",
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"memory_per_node": 65536,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 8,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_align_and_merge--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "ALIGN-AND-MERGE"
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},

‎recipes/clem-lif-to-stack-wrapper.json‎

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{
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"1": {
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"job_parameters": {
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"lif_file": "{lif_file}",
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"root_folder": "{root_folder}"
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},
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMLIFToStack -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "lif-to-stack",
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"memory_per_node": 65536,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 20,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_lif_to_stack--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "LIF2STACK"
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},
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"2": {
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"parameters": {
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"session_id": "{session_id}"
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},
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"queue": "{feedback_queue}",
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"service": "Murfey"
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},
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"start": [[1, []]]
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}

‎recipes/clem-lif-to-stack.json‎

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{
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"1": {
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"job_parameters": {
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"parameters": {
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"lif_file": "{lif_file}",
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"root_folder": "{root_folder}"
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},
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMLIFToStack -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "lif-to-stack",
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"memory_per_node": 65536,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 20,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_lif_to_stack--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "LIF2STACK"
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},

‎recipes/clem-tiff-to-stack-wrapper.json‎

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{
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"1": {
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"job_parameters": {
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"tiff_list": "{tiff_list}",
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"tiff_file": "{tiff_file}",
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"root_folder": "{root_folder}",
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"metadata": "{metadata}"
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},
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMTIFFToStack -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "tiff-to-stack",
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"memory_per_node": 32768,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 1,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_tiff_to_stack--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "TIFF2STACK"
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},
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"2": {
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"parameters": {
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"session_id": "{session_id}"
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},
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"queue": "{feedback_queue}",
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"service": "Murfey"
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},
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"start": [[1, []]]
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}

‎recipes/clem-tiff-to-stack.json‎

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{
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"1": {
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"job_parameters": {
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"parameters": {
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"tiff_list": "{tiff_list}",
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"tiff_file": "{tiff_file}",
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"root_folder": "{root_folder}",
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"output": {
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"murfey_feedback": 2
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},
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"parameters": {
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"cluster": {
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"commands": [
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"source /etc/profile.d/modules.sh",
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"module load EM/cryoem-services",
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"cryoemservices.wrap -w CLEMTIFFToStack -r \"$RECIPEWRAP\" -c {config_file} >runinfo 2>&1"
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],
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"cpus_per_task": 1,
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"environment": {
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"PATH": "/bin/:/usr/bin/:/usr/local/bin/",
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"USER": "{user}"
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},
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"job_name": "tiff-to-stack",
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"memory_per_node": 32768,
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"nodes": 1,
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"partition": "{partition}",
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"tasks": 1,
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"time_limit": "3:00:00"
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},
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"standard_error": "{session_dir}/tmp/run.err",
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"standard_output": "{session_dir}/tmp/run.out",
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"wrapper": "{session_dir}/tmp/.recipewrap--clem_tiff_to_stack--{job_name}",
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"workingdir": "{session_dir}/processed/"
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},
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"queue": "cluster.submission",
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"service": "TIFF2STACK"
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},

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