Man pages for rjbgoudie/mngr
Make, Rake, Workflows etc for R
| all_run_times | Parse all run times |
| arm_id | Unique name for arm |
| arms_factorial | Build factorial arms |
| cat_df | Concatenate and print a data.frame |
| copy_dir_retain_dates | Copy directories, retaining last modified dates of files |
| count_rout_errors | Count errors in file |
| count_rout_warnings | Count warnings in file |
| dir_git_toplevel | Get the toplevel git directory |
| dir_run_branch | Corresponding (branch-specific) run directory |
| dir_run_branch_toplevel | Toplevel directory of the (branch-specific) run directory |
| file_last_line | Get the final line of a file |
| file_path | Build a file path |
| find_mngrfile | Find Mngrfile |
| get_jobids | Extract Job ID from squeue output |
| git_abbrev_ref | Abbreviated name for HEAD commit in git repository |
| git_clone_or_pull | Clone or pull to the run dir |
| git_short_sha | Short SHA for HEAD commit in git repository |
| grapes-cores-grapes | Set the number of cores for a task |
| grapes-d-grapes | Set up task dependencies |
| grapes-hours-grapes | Set the number of hours for a task (walltime) |
| grapes-memory-grapes | Set the memory requirements for a task |
| grapes-merge-grapes | Merge arms |
| grapes-split-grapes | Split arms |
| grapes-task-grapes | Create a new task |
| grapes-throttle-grapes | Throttle the number of tasks to run simultaneously |
| hms | Convert seconds to formatted h:mm:ss string |
| is_inside_git_work_tree | Check if dir is inside git work tree |
| job_create | Create job |
| job_exists | Check for job existence |
| job_find_id | Find job id |
| kill_pattern | Kill Slurm jobs matching pattern |
| latest_logs | Summaries the latest R output |
| link_to_arm_indicies | Merge rout status table with arm data |
| lscheduler_add | Add to lscheduler |
| merge_tables | Merge squeue and rout status tables |
| mngr | Mngr |
| mngr_config | Set configuration options for mngr |
| mngr_option_dir_output | Converting run paths to output paths |
| mngr_option_dir_r_logs | Path to keep all R logs |
| mngr_option_dir_r_logs_latest | Path to keep the latest R logs |
| mngr_option_dir_run | Converting paths to runpaths |
| mngr_option_dir_slurm_logs | Path to keep Slurm logs |
| mngr_option_dir_state | Path to keep the state files |
| mngr_option_global_throttle | Global throttle setting |
| mngr_option_scheduler | Scheduler used for running R jobs |
| mngr_option_slurm_submit_path | Path to the directory containing Slurm submit script |
| mngr_option_use_tempfile | Save RDS data to a tempfile initially |
| monitor | Monitor Slurm jobs |
| monitor_logs | Print status of specified jobs |
| parse_name | Parse job names |
| parse_rout_files | Parse .Rout files to a data frame |
| pdf device | |
| pdf_file | path to pdf file |
| png | png device |
| png_file | path to png file |
| prereq_arm_ids | Arm IDs for the prerequisite tasks |
| pretty_print_arm_values | Print the arm values prettily |
| pretty_print_squeue | Pretty print squeue output |
| pretty_print_time | Pretty print the time |
| pretty_success_status | Pretty print ticks and crosses |
| qdel | A wrapper around Sluerm qdel |
| rds_file | path to rds file |
| read_rds_merge | Load and merge all RDS files |
| rfile | Add rfile as a slurm task |
| rfile_create | Create rfile task |
| rfiles | Add all R files in the current directory as tasks |
| run | Execute a task |
| run_jobs | Run jobs |
| run_time_seconds | Parse the run time of a file |
| save | save file |
| saveRDS | Save an R object to a rds file |
| sinfo | Information about slurm cluster |
| slurm_add_jobids | Add Job ID to list of Job IDs |
| slurm_summary | Return a brief summary of the Slurm queue status |
| squeue | Wrapper around Slurm's squeue function |
| startup | Startup mngr |
| sub_path | Manipuate a path |
| success | Determine whether R job ran successfully |
| system_in_dir | Evalutate system command in directory |
| task_create | Create task |
| task_exists | Check for task existence |
| task_get | Get a task |
| tiff | tiff device |
| tiff_file | path to tiff file |
| with_dir | Evaluate expression in a particular working directory |
