setup_run

Submitted by olange on Tue, 04/24/2012 - 19:25

Description:

generate run-director from a set of targets with existing setup

Usage:

setup_run.py	[-h] [-target_dir TARGET_DIR]
	[-target_prefix TARGET_PREFIX] [-quiet]
	[-flag_lib FLAG_LIB] [-label LABEL]
	[-method {abrelax,autoNOE,contacts,cyana,fixbb,rasrec,replica_dock,vanilla_dock}]
	[-remove [REMOVE [REMOVE ...]]] [-patch PATCH] -dir DIR
	[-run_label RUN_LABEL] [-job {interactive,moab,slurm}]
	[-database DATABASE] [-bin BIN] [-platform {linux,macos}]
	[-comp {gcc,icc}] [-extras {default,static,mpi}]
	[-overwrite] [-target [TARGETS [TARGETS ...]]]
	[-regenerate_derived_files] [-input INPUT] [-label2dir]
	[-traceback]

Detailed Help:

-h, --help	show this help message and exit
-target_dir TARGET_DIR	input-files are used from/put into this path, instead of directly into the run-directory
-target_prefix TARGET_PREFIX	target dirs are found here
-quiet	suppress output
-flag_lib FLAG_LIB	directory with meta files for generation of Rosetta cmd-line flag-files
-label LABEL	give a special label to this setup -- reflected in file-name for method-options
-method {abrelax,autoNOE,contacts,cyana,fixbb,rasrec,replica_dock,vanilla_dock}	choose algorithm; use together with -h to see additional method-specific options
-remove [REMOVE [REMOVE ...]]	remove one or more options from the SETUP
-patch PATCH	provide some python code that patches file-library content
-dir DIR	setup a run-directory here
-run_label RUN_LABEL	add this to the name of the directory
-job {interactive,moab,slurm}	run-scripts for which job-type? -- default all
-database DATABASE	rosetta database location
-bin BIN	rosetta binaries location
-platform {linux,macos}	which platform
-comp {gcc,icc}	which compiler
-extras {default,static,mpi}	which extras
-overwrite	overwrite run-directory
-target [TARGETS [TARGETS ...]], -targets [TARGETS [TARGETS ...]]	target_dir is target_prefix/target
-regenerate_derived_fi	files that are generated during processing of a method (e.g., *cst.centroid ) are regenerated
-input INPUT	look for previous results in this directory
-label2dir	instead of attaching target-label to target-name like this: target_label, create another subdirectory: target/label/run_label
-traceback	print full traceback in case of error

Examples:

setup_run.py -dir ~/structure_calculations/ -target t000_ -method rasrec -label with_rdc -job slurm
setup_run.py -dir run -target t000_ -method abrelax -extras default -job interactive
setup_run.py -dir ~/structure_calculations/ -target t000_ -method rasrec -run_label try_again -regenerate_derived_files

application:

setup_run