Command Line Tools

Fastr is shipped with a number of command line tools to perform common tasks and greatly simplify things such as debugging. The list of command line tools that is included in Fastr:




Print information from a job file


Dump the contents of a network run tempdir into a zip for remote assistance


Execute a fastr job file


Create a stub for a Tool based on a python script using argparse


Get PROV information from the result pickle.


Tiny wrapper in pylint so the output can be saved to a file (for test automation)


Print report of a job result (__fastr_result__.pickle.gz) file


Run a Network from the commandline


Command line access to the IOPlugin sink


Command line access to the IOPlugin source


Run the tests of a tool to verify the proper function


Trace samples/sinks from a run


Upgrade a fastr 2.x python file to fastr 3.x syntax


Verify fastr resources, at the moment only tool definitions are supported.

fastr cat

Extract selected information from the extra job info. The path is the selection of the data to retrieve. Every parts of the path (separated by a /) is seen as the index for the previous object. So for example to get the stdout of a job, you could use ‘fastr cat __fastr_extra_job_info__.json process/stdout’.

usage: fastr cat [-h] __fastr_extra_job_info__.json path

Positional Arguments


result file to cat


path of the data to print

fastr dump

Create a dump of a network run directory that contains the most important information for debugging. This includes a serialization of the network, all the job command and result files, the extra job information files and the provenance files. No data files will be included, but note that if jobs get sensitive information passed via the command line this will be included in the job files.

usage: fastr dump [-h] RUNDIR

Positional Arguments


The run directory to dump

The file to place the dump in

fastr execute

Execute a job from commandline.

usage: fastr execute [-h] [JOBFILE]

Positional Arguments


File of the job to execute (default ./__fastr_command__.yaml)

fastr extract_argparse

Extract basic information from argparse.

usage: fastr extract_argparse [-h] TOOL.xml

Positional Arguments

Python script to inspect


created Tool stub

fastr provenance

Export the provenance information from JSON to other formats or plot the provenance data as a graph.

usage: fastr provenance [-h] [-so SYNTAX_OUT_FILE] [-sf SYNTAX_FORMAT]
                        [-i INDENT] [-vo VISUALIZE_OUT_FILE]

Positional Arguments


File of the job to execute (default ./__fastr_prov__.json)

Named Arguments

-so, --syntax-out-file

Write the syntax to file.

-sf, --syntax-format

Choices are: [json], provn or xml

Default: “json”

-i, --indent

Indent size of the serialized documents.

Default: 2

-vo, --visualize-out-file

Visualize the provenance. The most preferred format is svg. You can specify any format pydot supports. Specify the format by postfixing the filename with an extension.

fastr pylint

Run pylint in such a way that the output is written to a file

usage: fastr pylint [-h] --output_file PYLINT.OUT

Named Arguments


The file to result in

fastr report

Print a report of a job result file.

usage: fastr report [-h] [-v] [JOBFILE]

Positional Arguments


File of the job to execute (default ./__fastr_result__.yaml)

Named Arguments

-v, --verbose

More verbose (e.g. add fastr job stdout and stderr)

Default: False

fastr run

Execute a job or network from commandline.

usage: fastr run [-h] NETWORKFILE

Positional Arguments


File of the network to execute

fastr sink

executes an ioplugin

usage: fastr sink [-h] -i INPUT [INPUT ...] -o OUTPUT [OUTPUT ...]
                  [-d DATATYPE [DATATYPE ...]]

Named Arguments

-i, --input

The url to process (can also be a list)

-o, --output

The output urls in vfs scheme (can also be a list and should be the same size as –inurl)

-d, --datatype

The datatype of the source/sink data to handle

fastr source

Executes an source command

usage: fastr source [-h] -i INPUT [INPUT ...] -o OUTPUT [-d DATATYPE]
                    [-s SAMPLE_ID]

Named Arguments

-i, --input

The url to process (can also be a list)

-o, --output

The output url in vfs scheme

-d, --datatype

The datatype of the source/sink data to handle

-s, --sample_id

The sample_id of the source/sink data to handle

fastr test

Run a tests for a fastr resource.

usage: fastr test [-h] {tool,tools,network,networks} ...



Test a single tool

fastr test tool [-h] TOOL
Positional Arguments

Tool to test or directory with tool reference data


Test all tools known to fastr

fastr test tools [-h]


Test a single network

fastr test network [-h] NETWORK
Positional Arguments

The reference data to test the Network


Test all network references inside subdirectories

fastr test networks [-h] [--result RESULT.json] REFERENCE
Positional Arguments

path of the directory containing subdirectories with reference data

Named Arguments

Write the results of the test to a JSON file

fastr trace

Fastr trace helps you inspect the staging directory of the Network run and pinpoint the errors.

usage: fastr trace [-h] [--verbose] [--sinks [SINKS [SINKS ...]]]
                   [--samples [SAMPLES [SAMPLES ...]]]

Positional Arguments


result file to cat

Default: “/home/docs/checkouts/”

Named Arguments

--verbose, -v

set verbose output for more details

Default: False


list results for specified sinks


list result for all samples

fastr upgrade

Upgrades a python file that creates a Network to the new fastr 3.x syntax. The file will be parsed and the full syntax tree will be transformed to fit the new syntax.


Solves most common problems, but cannot always solve 100% of the issues

usage: fastr upgrade [-h] [--type TYPE]

Positional Arguments

Network creation file (in python) to upgrade

location of the result file

Named Arguments


tool of resource to upgrade, one of: network, tool

fastr verify

Verify fastr resources, at the moment only tool definitionsare supported.

usage: fastr verify [-h] [--createtest] TYPE path

Positional Arguments


Possible choices: tool

Type of resource to verify (e.g. tool)


path of the resource to verify

Named Arguments

--createtest, -c

Create a reference result for a tool test

Default: False