as.character | Convert task object to character, can be dumped to file and... |
bcmd | Returns vector of bsub (ie LSF) commands associated with this... |
bjobs | Tracks down any LSF jobs associated with this Job object... |
bkill | Kills any running LSF jobs associated with this Job object |
brun | Runs jobs on LSF |
bsub_cmd | bsub_cmd |
c | Concatenates Job objects built from the same Task |
cache | caches .rds copy of job object to standard location... |
chmod | chmods Job output directories Chmods outputs of jobs (by... |
cmd | Gets vector of command line calls associated with the jobs in... |
cores | Gets cores associated with the jobs in the Job object |
cores-set | Sets cores associated with the jobs in the Job object |
dedup | dedup |
dirs | returns list of character vectors containing the contents of... |
entities | returns original keyed data.table of entities associated with... |
err | returns vector of paths to stderr files associated with this... |
file.dir | file.dir |
file.name | file.name |
Flow | Flow |
FlowAnnotation | Creates an entity-specific annotation object (ie a path or... |
FlowAnnotation-class | Class to represent an entity-specific annotation (ie a path... |
Flow-class | Class representing a collection of tasks |
FlowLiteral | Creates object representing a literal argument to a task (ie... |
FlowLiteral-class | Class to represent a literal argument to a task (ie a static... |
FlowOutput | Constructs an object representing the wiring of a regexp on a... |
FlowOutput-class | Class representing the wiring of a regexp on a job output... |
gres | Gets queue or partition associated with the jobs in the Job... |
gres-set | Sets qos associated with the jobs in the Job object |
ids | returns vector of entity ids associated with this Job objedct |
inputs | returns keyed data.table of inputs annotation associated with... |
io_c | Gets ionice -c |
io_c-set | Sets ionice parameters associated with Job object |
io_n | Gets ionice -n |
io_n-set | Sets ionice parameters associated with Job object |
jname | Returns character vector of job names associated with this... |
Job | Constructs a job object from a Task and keyed data.table of... |
Job-class | Class representing a set of jobs, each which is the... |
key | Retrieves the entity key associated with this Job object |
length | returns length of this Job object |
mem | Gets max memory associated with the jobs in the Job object |
mem-set | Sets max memory associated with the jobs in the Job object |
module | Class to implement modules, which are standalone pieces of... |
Module-class | Module class |
module-task | Gets module associated with a Task |
more | more |
nice_val | Gets nice value |
nice_val-set | Sets nice value associated with job object |
normalizePath | normalizePath |
now | Toggles whether to force jobs to run now |
now-set | Sets now param associated with the jobs in the Job object |
out | returns vector of paths to stdout files associated with this... |
outdir | Gets vector of output directories associated with the jobs in... |
outputs | returns keyed data.table of output entity annotations... |
parse.info | parse.info |
plot.Flow | plot.Flow |
purge | purges all output / run directories associated with this Job... |
qcmd | Returns vector of qsub (ie SGE) commands associated with this... |
qjobs | Tracks down any sGE jobs associated with this Job object... |
qkill | Kills any running SGE jobs associated with this Job object |
qos-set | Sets qos associated with the jobs in the Job object |
qprior | Gets qprior value |
qprior-set | Sets qprior parameter associated with job object |
qrun | Runs jobs on LSF |
qsub_cmd | qsub_cmd |
queue | Gets queue associated with the jobs in the Job object |
queue-set | Sets queue associated with the jobs in the Job object |
refresh | refreshes .rds copy of job object from standard location... |
report | Retrieves a data.table reporting detailed runtime stats... |
reset.job | reset.job Reset a job with different params |
rrbind | rrbind |
run | Runs jobs as local commands from shell via R system calls |
scmd | Returns vector of ssub (ie Slurm) commands associated with... |
setwd | changes directory to the directory of the job |
silent | run expression without any printed output execute expression... |
sjobs | Tracks down any slurm jobs associated with this Job object... |
skill | Kills any running Slurm jobs associated with this Job object |
Slurmize | updates cmd.sh to run on slurm |
sniff | sniff |
srun | Runs jobs on Slurm |
ssub_cmd | ssub_cmd |
status | Returns character vector of status of jobs in this Job... |
status.info | returns vector of more detailed statuses associated with jobs... |
sub | caches .rds copy of job object to standard location... |
sub-.Flow | Flow subset |
tailf | tailf |
task | Object representing a task, which is a wiring of a module... |
Task-class | S4 class for 'Task' |
tasks | returns original keyed data.table of entities associated with... |
time | Gets max time limit associated with job object |
time-set | Sets max time limit associated with the jobs in the Job... |
update | updates Job status This method checks inputs for updates to... |
viewtask | or Flow Task object |
xml2task | Makes a best attempt to convert a firehose xml task... |
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