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

Usage: [-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]

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