Getting started with gkno
See the instructions on how to download and install gkno and the instructions to determine how to use the help options in gkno to find the pipeline that is most relevant to your analysis. If no pipelines exist that perform the tasks required, you can either construct your own pipeline using the provided instructions or contact me at AlistairNWard@gmail.com or on Twitter at @AlistairNWard.
Executing a pipeline
Executing a pipeline is simple; all we need is to run gkno and tell it the pipeline we want to use. When running a pipeline for the first time, it is a good idea to look at the help information and see exactly what the pipeline does (the workflow), what arguments it accepts, and in particular, what parameter sets are available.
gkno arguments
There is a set of arguments that can be applied to any pipeline that perform functions that are pipeline independent. This includes functions such as selecting or creating parameter sets, allowing parallel execution of tasks etc. To see a list of these commands, use the --gkno-arguments (-ga) argument. Click below to see all of the available commands, or a more detailed description is provided here.
  • --all-pipelines
  • -api
  • flag
  • Print all available pipelines to screen.
  • --categories
  • -cat
  • flag
  • Display all available help categories.
  • --configuration-path
  • -cp
  • string
  • Define the path to the directory in which the configuration file(s) resides.
  • --debug
  • -db
  • flag
  • Display debugging information.
  • --do-not-execute
  • -dne
  • flag
  • Flag to stop execution of the Makefile after gkno is run.
  • --do-not-log-usage
  • -dnl
  • flag
  • Do not log this run of gkno.
  • --do-not-reorder
  • -dnr
  • flag
  • Flag to disable reordering of values supplied to linked arguments.
  • --draw-full-pipeline-graph
  • -dfpg
  • string
  • Name of the file to which a full visual depiction of the pipeline graph will be output.
  • --draw-pipeline-graph
  • -dpg
  • string
  • A full and reduced version of the pipeline graph will be output to files beginning with this value and appended with '-full' and '-reduced'.
  • --draw-reduced-pipeline-graph
  • -drpg
  • string
  • Name of the file to which a reduced visual depiction of the pipeline graph will be output. This is the form of the pipeline shown on the webpage for the pipeline.
  • --export-parameter-set
  • -ep
  • string
  • Export a parameter set to a configuration file of this name.
  • --gkno-arguments
  • -ga
  • flag
  • Print help information for gkno arguments.
  • --help
  • -h
  • flag
  • Print requested help message.
  • --input-path
  • -ip
  • string
  • Path for input files if not defined. Default: current directory.
  • --makefile-id
  • -mi
  • string
  • Append this text to all makefiles generated in this execution of gkno.
  • --multiple-makefiles
  • -mm
  • flag
  • If any of the long form arguments are supplied with a list of valuess causing one or more tools to require multiple iterations, if this is set to true, multiple makefiles are generated. If set to false [default], a single makefile will be generated.
  • --number-jobs
  • -nj
  • integer
  • The number of parallel jobs to be used (only valid in conjunction with the --internal-loop option).
  • --output-path
  • -op
  • string
  • Path for output files if not defined. Default: current directory.
  • --parameter-set
  • -ps
  • string
  • Generate a stdout and stderr for each task.
  • --remove-parameter-set
  • -rp
  • string
  • Remove a user-generated parameter set.
  • --web-content
  • -web
  • flag
  • Write out json files for use with the web page.