Provided by: datalad_0.11.2-2_all bug

NAME

       datalad run - run an arbitrary shell command and record its impact on a dataset.

SYNOPSIS

       datalad  run  [-h]  [-d  DATASET]  [-i  PATH]  [-o  PATH]  [--expand  WHICH]  [--explicit]
              [-m MESSAGE] [--sidecar yes|no] [--rerun] ...

DESCRIPTION

       It is recommended to craft the command such that it can run in the root directory  of  the
       dataset  that the command will be recorded in. However, as long as the command is executed
       somewhere underneath the dataset root, the exact location will be recorded relative to the
       dataset root.

       If  the  executed  command  did not alter the dataset in any way, no record of the command
       execution is made.

       If the given command errors, a COMMANDERROR exception with the  same  exit  code  will  be
       raised, and no modifications will be saved.

   Command format
       A  few  placeholders are supported in the command via Python format specification. "{pwd}"
       will be replaced with the full path of the current working directory. "{dspath}"  will  be
       replaced  with  the  full  path  of  the  dataset  that  run is invoked on. "{inputs}" and
       "{outputs}" represent the values specified by --input and --output. If multiple values are
       specified,  the  values will be joined by a space. The order of the values will match that
       order from the command line, with any globs expanded in alphabetical  order  (like  bash).
       Individual values can be accessed with an integer index (e.g., "{inputs[0]}").

       Note  that  the  representation  of  the inputs or outputs in the formatted command string
       depends on whether the command is given as a list of arguments  or  as  a  string  (quotes
       surrounding the command). The concatenated list of inputs or outputs will be surrounded by
       quotes when the command is given as a list but not when it is  given  as  a  string.  This
       means  that  the  string  form  is  required  if you need to pass each input as a separate
       argument to a preceding script (i.e., write the command  as  "./script  {inputs}",  quotes
       included). The string form should also be used if the input or output paths contain spaces
       or other characters that need to be escaped.

       To escape a brace character, double it (i.e., "{{" or "}}").

       Custom    placeholders    can    be    added    as    configuration    variables     under
       "datalad.run.substitutions".  As an example:

       Add a placeholder "name" with the value "joe"::

         % git config --file=.datalad/config datalad.run.substitutions.name joe
         % datalad add -m "Configure name placeholder" .datalad/config

       Access the new placeholder in a command::

         % datalad run "echo my name is {name} >me"

OPTIONS

       COMMAND
              command for execution. A leading '--' can be used to disambiguate this command from
              the preceding options to DataLad. [Default: None]

       -h, --help, --help-np
              show this help message. --help-np forcefully  disables  the  use  of  a  pager  for
              displaying the help message

       -d DATASET, --dataset DATASET
              specify  the  dataset  to  record  the  command  results  in. An attempt is made to
              identify the dataset based on the current working directory. If a dataset is given,
              the  command  will  be executed in the root directory of this dataset. Constraints:
              Value must be a Dataset or a valid identifier of a Dataset (e.g. a path)  [Default:
              None]

       -i PATH, --input PATH
              A dependency for the run. Before running the command, the content of this file will
              be retrieved. A value of "." means "run datalad get .". The value  can  also  be  a
              glob. This option can be given more than once. [Default: None]

       -o PATH, --output PATH
              Prepare  this  file  to be an output file of the command. A value of "." means "run
              datalad unlock ." (and will fail if some content  isn't  present).  For  any  other
              value,  if  the content of this file is present, unlock the file. Otherwise, remove
              it. The value can also be a  glob.  This  option  can  be  given  more  than  once.
              [Default: None]

       --expand WHICH
              Expand globs when storing inputs and/or outputs in the commit message. Constraints:
              value must be NONE, or value must be one of ('inputs', 'outputs', 'both') [Default:
              None]

       --explicit
              Consider  the specification of inputs and outputs to be explicit. Don't warn if the
              repository is dirty, and only save modifications to the listed  outputs.  [Default:
              False]

       -m MESSAGE, --message MESSAGE
              a  description  of  the  state or the changes made to a dataset. Constraints: value
              must be a string [Default: None]

       --sidecar yes|no
              By default,  the  configuration  variable  'datalad.run.record-sidecar'  determines
              whether  a  record  with  information  on  a  command's  execution is placed into a
              separate record file instead of the commit message (default: off). This option  can
              be  used to override the configured behavior on a case-by-case basis. Sidecar files
              are placed into the dataset's '.datalad/runinfo' directory  (customizable  via  the
              'datalad.run.record-directory'  configuration variable). Constraints: value must be
              NONE, or value must be convertible to type bool [Default: None]

       --rerun
              re-run the command recorded in the last saved change (if any). Note: This option is
              deprecated since version 0.9.2 and will be removed in a later release. Use `datalad
              rerun` instead. [Default: False]

AUTHORS

        datalad is developed by The DataLad Team and Contributors <team@datalad.org>.

                                            2019-02-09                             datalad run(1)