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spipe - simple pipeline running interface


version 0.9.1


spipe [--version | [-?|-h|--help] | [-g|--debug] | [--graphviz | [-c|--config file | [[-d|--directory value] | [-i|--input string| [-it|--itype string | [[--start value] | [[--stop value]

  spipe -config t/data/string_manipulation.yml -d /tmp/test


Spipe is a control script for running simple pipelines read from configuration files written in YAML language.

For internal details of the pipeline, check the documentation for the perl module App::Pipeline::Simple.


spipe - simple pipeline running interface


-v | --version

Print out a line with the program name and version number.

-? | -h | --help

Show this help.

-g | --debug

Print out the UNIX command line equivalent of the pipeline and exit.

Reports parsing and logical errors.


Print out a graphviz dot file.

Example one liner to display a graph of the pipeline:

  spipe -config t/data/string_manipulation.yml -graph > \
  /tmp/; dot -Tpng /tmp/| display
-c | --config string

Path to the config file. Required unless there is a file called config.yml in the current directory.

-d | --directory string

Directory to keep all files.

If the directory does not exist, it will be created and a copy of the config file will be copied into it under name config.yml.

For subsequent runs of the that pipeline, you adjust the parameters in the configuration file and rerun spipe without -config and -directory options.

-i | --input string

Optional input to pipeline.

-it | --itype string

Type of the optional input. Values?

--start string

ID of the step to start or restart the pipeline.

Fails if the prerequisites of the step are not met, i.e. the input file(s) does not exist.

--stop string

ID of the step to stop the pipeline. Defaults to the last step.

--verbose int

Verbosity level. Defaults to zero. This will get translated to Log::Log4perl levels:

  verbose   =  -1    0     1     2
  log level =  DEBUG INFO  WARN  ERROR


Example run:

  spipe -config t/data/string_manipulation.xml -dir /tmp/test

reads instructions from the config file and writes all information to the project directory.

The debug option will parse the config file, print out the command line equivalents of all commands and print out warnings of problems encountered in the file:

  spipe -config t/data/string_manipulation.xml -dir /tmp/test

An other tool integrated in the system is visualization of the execution graph. It is done with the help of GraphViz perl interface module that will need to be installed from CPAN.

The following command line creates a Graphviz dot file, converts it into an image file and opens it with the Imagemagic display program:

  spipe -config t/data/string_manipulation.xml -graph > \
    /tmp/; dot -Tpng /tmp/ | display


The default configuration is written in YAML, a simple and human readable language that can be parsed in many languages cleanly into data structures.

The YAML file contains four top level keys for the hash that the file will be read into: 1) name to give the pipeline a short name, 2) version to indicate the version number, 3) description to give a more verbose explanation what the pipeline does, and 4) steps listing pipeline steps.

  description: "Example of a pipeline"
  name: String Manipulation
  version: '0.4'

Each step is identified by an unique short ID and has a name that identifies an executable somewhere in the system path. Alternatively, you can give the full path leading to the executable file with key path. The name will be added to the path and padded with a suitable separator character when needed.

Arguments to the executable are given individually as key/value pairs within the args tag. A single hyphen is added in front of the argument key when they are executed. If two hyphens are needed, just add one the key. Arguments can exist without values, too.

    name: cat
        type: redir
        value: s1.txt
        type: redir
        value: s3_mod.txt
      - s4

There are two special keys in and out that need to have a key type defined. The IO type can get several kinds of values:


that indicates that the argument is an unnamed argument to the executable


will be interpreted as UNIX redirection character '&lt' or '&gt' depending on the context


means that IO happens from/to a file and is rendered as named argument


is rendered like file, but is a mnemonic that all files under this directory name are processed

Finally, the step tag can contain the next key that gives an array of IDs for the next steps in the execution. Typically, these steps depend on the previous step for input.

Practices that are completely bonkers, like spaces in file names, are not supported.

Finally, it is worth noting that YAML can need escaping and quoting to get special characters inside strings. Double quotes around a string works most of the time well. A single quote inside a single quoted string needs to be doubled.

The following example of a perl one-liner (Thanks to Nic Walker for alerting me) could be equally well written using double quotes like this: "'print $F[1]'"

    name: perl
      lane: '''print $F[1]'''
        type: redir
        value: myfile
        type: redir
        value: sec_column

Advanced features

The pipeline does not have to be linear; it can contain branches. For example, the pipeline can have several start points with different kinds of input: file and string.

Sometimes it is useful to run the same pipeline with different parameter. The starting point of execution can take a value from the command line. Leave the value for the given argument blank in the configuration file and give it from the command line. Matching of values is done by matching the type string.

  spipe -conf input_demo.yml --input=ABC --itype=str

  description: "Demonstrate input from command line"
  name: input.yml
  version: '0.1'
      name: echo
          type: unnamed
          type: redir
          value: s1_string.txt

The empty value will be filled in from the command line into the config.yml stored in the project directory. Also, the config file looks slightly different since the steps are written out as App::Pipeline::Simple objects. Functionally there is no difference.


This pipeline engine has been tested using mostly linear pipelines. Extensive branching and complex dependencies might not work as expected.

There are no explicit tests for the existence of step input files. Scripts are expected to run these steps themselves and die gracefully when appropriate.

There has been no attempt to execute steps in parallel fashion.

If all this is included, this pipeline engine might not be "simple" any more.




Heikki Lehvaslaiho, KAUST (King Abdullah University of Science and Technology).


This software is copyright (c) 2012 by Heikki Lehvaslaiho.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

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