| run {flowr} | R Documentation |
Run complete pipelines, by wrapping several steps into one convinient function.
NOTE: please use flowr version 0.9.8.9010 or higher.
In summary, this function performs the following steps:
the argument x defines the name of the pipeline.
Say, for example sleep_pipe.
fetch_pipes: finds the pipeline definition
(sleep_pipe.R, sleep_pipe.def and
sleep_pipe.conf files)
sleep_pipe(...): Create all the required commands
(flowmat)
to_flow: Use flowmat and
sleep_pipe.def to create a flow object.
submit_flow: Submit the flow to the cluster.
run(x, platform, def, conf, wd = opts_flow$get("flow_run_path"),
flow_run_path = wd, rerun_wd, start_from, execute = FALSE, ...)
run_pipe(x, platform, def, conf, wd = opts_flow$get("flow_run_path"),
flow_run_path = wd, rerun_wd, start_from, execute = FALSE, ...)
x |
name of the pipeline to run. This is a function called to create a flow_mat. |
platform |
what platform to use, overrides flowdef |
def |
flow definition |
conf |
a tab-delimited configuration file with path to tools and default parameters. See fetch_pipes. |
wd |
an alias to flow_run_path |
flow_run_path |
passed onto to_flow. Default it picked up from flowr.conf. Typically this is ~/flowr/runs |
rerun_wd |
if you need to run, supply the previous working dir |
start_from |
the step to start a rerun from. Intitutively, this is ignored in a fresh run and only used in re-running a pipeline. |
execute |
TRUE/FALSE |
... |
passed onto the pipeline function as specified in x |
## Not run:
## Run a short pipeline (dry run)
run("sleep_pipe")
## Run a short pipeline on the local machine
run("sleep_pipe", platform = "local", execute = TRUE)
## Run a short pipeline on the a torque cluster (qsub)
run("sleep_pipe", platform = "torque", execute = TRUE)
## Run a short pipeline on the a MOAB cluster (msub)
run("sleep_pipe", platform = "moab", execute = TRUE)
## Run a short pipeline on the a IBM (LSF) cluster (bsub)
run("sleep_pipe", platform = "lsf", execute = TRUE)
## Run a short pipeline on the a MOAB cluster (msub)
run("sleep_pipe", platform = "moab", execute = TRUE)
## change parameters of the pipeline
## All extra parameters are passed on to the function function.
run("sleep_pipe", platform = "lsf", execute = TRUE, x = 5)
## End(Not run)