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Merge pull request #757 from datalad-handbook/fixlinks
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Fixlinks
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adswa authored Sep 2, 2021
2 parents 456ebde + 6f6093a commit 520059f
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4 changes: 2 additions & 2 deletions docs/basics/101-138-sharethirdparty.rst
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Expand Up @@ -570,10 +570,10 @@ be able to fetch content from the tarball shared on Figshare via DataLad.
.. rubric:: Footnotes
.. [#f1] :term:`GitLab`, on the other hand, provides a git-annex configuration. It
.. [#f1] Older versions of :term:`GitLab`, on the other hand, provide a git-annex configuration. It
is disabled by default, and to enable it you would need to have administrative
access to the server and client side of your GitLab instance. Find out more
`here <https://docs.gitlab.com/ee/administration/git_annex.html>`_.
`here <https://docs.gitlab.com/12.10/ee/administration/git_annex.html>`_.
Alternatively, GitHub can integrate with
`GitLFS <https://git-lfs.github.com/>`__, a non-free, centralized service
that allows to store large file contents. The last paragraph in this
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2 changes: 1 addition & 1 deletion docs/beyond_basics/101-171-enki.rst
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Expand Up @@ -79,7 +79,7 @@ Also note that there is a large collection of pre-existing container datasets av

During a :command:`datalad containers-run` command, the ``--call-fmt`` specification will be used to call the container.
The placeholders ``{img}`` and ``{cmd}`` will be replaced with the container (``{img}``) and the command given to ``datalad containers-run`` (``{cmd}``).
Thus, the ``--cleanenv`` flag (`recommended by fMRIprep <https://fmriprep.org/en/stable/singularity.html#handling-environment-variables>`_) as well as bind-mounts are handled prior to the container invocation, and the ``--fs-license-file`` option with a path to the license file within the container is appended to the command.
Thus, the ``--cleanenv`` flag as well as bind-mounts are handled prior to the container invocation, and the ``--fs-license-file`` option with a path to the license file within the container is appended to the command.
Bind-mounting the working directory (``-B "$PWD"``) makes sure to bind mount the directory from which the container is being called, which should be the superdataset that contains input data and ``pipelines`` subdataset.
With these bind-mounts, input data and the freesurfer license file within ``pipelines`` are available in the container.

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