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Verified Commit 601638e8 authored by Xavier Robin's avatar Xavier Robin
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Revert "doc: activate notes syntax"

This reverts commit ab9bc19e.
Didn't work on our GitLab instance.
parent ab9bc19e
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OST Docker
==========
> [!note]
> For most docker installations it is required to run docker commands as root. As
> this depends on set up, we skip the ``sudo`` in all commands.
.. note::
  • I think that **Note:** instead of .. note:: could work as a workaround to at least mark the area.

  • Btw if you edit the file in the web interface you can preview the markdown.

  • Author Maintainer

    Indeed, Edit > Edit single file comes with a preview. I had clicked on the link to the IDE where I could not find a preview.

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For most docker installations it is required to run docker commands as root. As
this depends on set up, we skip the ``sudo`` in all commands.
Obtain Docker image from the OST registry
-----------------------------------------
......@@ -62,13 +63,14 @@ As the last line you should see ``OST is working!``.
Run script and action with OST
------------------------------
> [!note]
> If script or action requires some external files eg. PDBs, they have to be located in the
> path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
> path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
> a script.py in /home/user we could mount the /home/user to /home in docker as
> above by specifying -v /home/user:/home. To run the script we thus need to
> provide the (relative) path to the script and (relative) path to the file eg:
.. note::
If script or action requires some external files eg. PDBs, they have to be located in the
path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
a script.py in /home/user we could mount the /home/user to /home in docker as
above by specifying -v /home/user:/home. To run the script we thus need to
provide the (relative) path to the script and (relative) path to the file eg:
.. code-block:: bash
......@@ -184,8 +186,9 @@ Eg. to run molck type:
docker run --rm -ti --entrypoint molck <IMAGE NAME> --help
> [!note]
> Note how the options to the command are specified after the image name.
.. note::
Note how the options to the command are specified after the image name.
.. _docker_compound_lib:
......
......
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