R: Run automated Pipelines

run {flowr} | R Documentation

## Run automated Pipelines

### Description

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.

### Usage

    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, ...)

### Arguments

`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

### Examples

    ## 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)

[Package flowr version 0.9.10 Index]