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Included srun_settings fields in scratch_copy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,60 +1,65 @@ | ||
| { | ||
| "global":{ | ||
| "data_path": "/data/bi", | ||
| "archived_path": "/archived/bi", | ||
| "yaml_conf_path": "~/buisciii_config.yml" | ||
| "global": { | ||
| "data_path": "/data/bi", | ||
| "archived_path": "/archived/bi", | ||
| "yaml_conf_path": "~/buisciii_config.yml" | ||
| }, | ||
| "sftp_copy": { | ||
| "protocol": "rsync", | ||
| "options": ["-rlpv", "--update", "-L", "--inplace"], | ||
| "exclusions": [ | ||
| "'*_NC'", | ||
| "'lablog'", | ||
| "'work'", | ||
| "'00-reads'", | ||
| "'*.sh'", | ||
| "'.nextflow*'", | ||
| "'*_DEL'", | ||
| "'*.R'", | ||
| "'*.py'" | ||
| ] | ||
| "protocol": "rsync", | ||
| "options": ["-rlpv", "--update", "-L", "--inplace"], | ||
| "exclusions": [ | ||
| "'*_NC'", | ||
| "'lablog'", | ||
| "'work'", | ||
| "'00-reads'", | ||
| "'*.sh'", | ||
| "'.nextflow*'", | ||
| "'*_DEL'", | ||
| "'*.R'", | ||
| "'*.py'" | ||
| ] | ||
| }, | ||
| "xtutatis_api_settings": { | ||
| "api_url": "/drylab/api/", | ||
| "server": "http://iskylimsapi.isciiides.es" | ||
| "api_url": "/drylab/api/", | ||
| "server": "http://iskylims.isciiides.es" | ||
| }, | ||
| "api_settings": { | ||
| "server": "http://iskylims.isciiides.es", | ||
| "api_url": "/drylab/api/" | ||
| }, | ||
| "bioinfo_doc": { | ||
| "bioinfodoc_path": "/data/bioinfo_doc/", | ||
| "services_path": "services", | ||
| "service_folder": ["service_info", "result"], | ||
| "service_info_template_path_file" : "templates/jinja_template_service_info.j2", | ||
| "delivery_template_path_file" : "templates/jinja_template_delivery.j2", | ||
| "html_template_path_file" : "templates/html_service_template.html", | ||
| "path_to_css" : "assets/css", | ||
| "wkhtmltopdf_path" : "/data/bi/pipelines/miniconda3/envs/buisciii-tools/bin/wkhtmltopdf", | ||
| "email_host":"mx2.isciii.es", | ||
| "email_port" : "587", | ||
| "email_host_user" : "[email protected]", | ||
| "email_use_tls" : "True" | ||
| "bioinfodoc_path": "/data/bioinfo_doc/", | ||
| "services_path": "services", | ||
| "service_folder": ["service_info", "result"], | ||
| "service_info_template_path_file": "templates/jinja_template_service_info.j2", | ||
| "delivery_template_path_file": "templates/jinja_template_delivery.j2", | ||
| "html_template_path_file": "templates/html_service_template.html", | ||
| "path_to_css": "assets/css", | ||
| "wkhtmltopdf_path": "/data/bi/pipelines/miniconda3/envs/buisciii-tools/bin/wkhtmltopdf", | ||
| "email_host": "mx2.isciii.es", | ||
| "email_port": "587", | ||
| "email_host_user": "[email protected]", | ||
| "email_use_tls": "True" | ||
| }, | ||
| "new_service": { | ||
| "fastq_repo": "/srv/fastq_repo" | ||
| "fastq_repo": "/srv/fastq_repo" | ||
| }, | ||
| "scratch_copy": { | ||
| "protocol": "rsync", | ||
| "options": ["-rlpv"], | ||
| "exclusions": [ | ||
| "'*_NC'", | ||
| "'service_info.txt'", | ||
| "'work'" | ||
| ] | ||
| "protocol": "rsync", | ||
| "options": ["-rlpv"], | ||
| "exclusions": [ | ||
| "'*_NC'", | ||
| "'service_info.txt'", | ||
| "'work'" | ||
| ], | ||
| "srun_settings": { | ||
| "--partition": "middle_idx", | ||
| "--time": "24:00:00", | ||
| "--chdir": "/scratch/bi/" | ||
| } | ||
| }, | ||
| "archive": { | ||
| "protocol": "rsync", | ||
| "options": ["-rv"] | ||
| "protocol": "rsync", | ||
| "options": ["-rv"] | ||
| } | ||
| } | ||
| } |