The run command

Synopsis

    bpipe execute [-h] [-t] [-d <output folder>] [-v] [-r] <pipeline> [<input 1>, <input 2>,...]

Options

The execute command accepts the same options as the [run] command.

Note: If you want to run in test mode (to see what commands will be executed before running them), supply the -t option.

Description

Creates a Bpipe job for a pipeline defined on the command line and runs it. This command causes the same behavior invoked by the run command, except that the pipeline is not defined in a file but rather on the command line itself. Since there is no way to define pipeline stages, all the stages used must be defined by automatically loaded pipeline stages that are present in files in the Bpipe lib directory (by default, ~/bpipes, or you can set the $BPIPE_LIB environment variable to change it. Alternatively, supply the -s option to cause Bpipe to load pipeline stages from a file explicitly.

Example 1 - Run an Ad Hoc Pipeline

Create a file called stages.groovy with the following contents:

hello = {
  exec 'echo hello'
}

world = {
  exec 'echo world'
}

Then execute:

  bpipe execute -s stages.groovy 'hello + world'

This behaves the same as creating a file, test.groovy:

  run { hello + world }

And running it using:

  bpipe run test.groovy

Example 2 - Run a Single Stage

Create a file called stages.groovy with the following contents:

hello = {
  exec "cp $input $output"
}

world = {
  exec 'echo world'
}

Then execute a single stage from this file:

  echo hello > test.txt
  bpipe execute -s stages.groovy hello test.txt