Merge pull request #322 from FCP-INDI/known_issue_bids-validator

📝 Known issue: ``bids-validator: command not found``

docs/_sources/user/help.rst

@@ -45,6 +45,11 @@ where :file:`crash-file.pklz` is the name of the crash file you wish to view.
 Common Issues
 ^^^^^^^^^^^^^
 
+``bids-validator: command not found``
+-------------------------------------
+
+.. include:: /user/known-issues/FCP-INDI/C-PAC/2110.rst
+
 My end-to-end surface pipeline with ABCD post-processing is hanging/stalling.
 -----------------------------------------------------------------------------
 

docs/_sources/user/known-issues/FCP-INDI/C-PAC/2110.rst

@@ -0,0 +1,26 @@
+..
+   The headings here start with * to nest under - in user/help
+
+``bids-validator`` is missing from C-PAC image
+**********************************************
+
+.. versionadded:: 1.8.6
+
+See issue :issue:`2110` for the latest developments on this issue.
+
+When running C-PAC with an input BIDS directory, no data configuration file and without the ``--skip_bids_validator`` flag, C-PAC will crash with a ``bids-validator: command not found`` message.
+
+Workarounds
+###########
+
+Either of these workarounds should allow you to run versions of C-PAC affected by this issue:
+
+- Add the ``--skip_bids_validator`` flag to your run command. If desired, run the `BIDS validator`_ on your input data prior to using C-PAC.
+- Use a :doc:`data configuration file </user/subject_list_config>` to specify your input data.
+
+Planned resolution
+``````````````````
+
+- Restoring or replacing ``bids-validator`` in an upcoming version of C-PAC.
+
+.. _BIDS validator: https://github.com/bids-standard/bids-validator#readme