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17 changes: 14 additions & 3 deletions docs/_writing_dependencies_conda.rst
Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,17 @@ As configured by Planemo, when Galaxy encounters these ``requirement`` tags it
will attempt to install Conda, check for referenced packages (such as
``seqtk``), and install them as needed for tool testing.

.. figure:: images/dependency_resolution.png
:alt: Diagram describing mapping tool requirements to dependencies.

Galaxy's dependency resolution maps tool requirement tags to concrete
applications and libraries setup by the Galaxy deployer (or Planemo). As
the above diagram indicates the same requirements may be used by multiple
Galaxy tools and a single Galaxy tool may depend on multiple requirements.
The document describes working with Conda dependencies from a developer
perspective but other dependency resolution techniques are covered in
the `Galaxy docs <https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html>`__.

We can check if the requirements on a tool are available in best practice
Conda channels using an extended form of the ``planemo lint`` command. Passing
``--conda_requirements`` flag will ensure all listed requirements are found.
Expand All @@ -88,8 +99,8 @@ Conda channels using an extended form of the ``planemo lint`` command. Passing
.. INFO: Requirement [seqtk@1.2] matches target in best practice Conda channel [bioconda].


.. note:: You can download the final version of the seqtk from the Planemo tutorial using
the command::
.. note:: You can download the final version of the seqtk seq wrapper from the Planemo
tutorial using the command::

$ planemo project_init --template=seqtk_complete seqtk_example
$ cd seqtk_example
Expand Down Expand Up @@ -136,7 +147,7 @@ for their declared requirements.
seqtk not found
$

The above install worked properly, but seqtk is not on your ``PATH`` because this merely
The above install worked properly, but ``seqtk`` is not on your ``PATH`` because this merely
created an environment within the Conda directory for the seqtk installation. Planemo
will configure Galaxy to exploit this installation. If you wish to interactively explore
the resulting enviornment to explore the installed tool or produce test data the output
Expand Down
Binary file added docs/images/dependency_resolution.png
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