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Link from the 16.01 announcement to the Admin wheels documentation,
document the process of adding new wheels.
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@@ -1,3 +1,5 @@
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.. _framework-dependencies:
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Galaxy Framework Dependencies
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=============================
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@@ -567,8 +569,46 @@ complete.
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Adding additional wheels as Galaxy dependencies
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-----------------------------------------------
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**TODO**
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New wheels can be added to Galaxy, or the versions of existing wheels can be
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updated, using `Galaxy Starforge`_, Galaxy's Docker-based build system.
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For the time being, see the `Galaxy Starforge`_ documentation.
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The process is still under development and will be streamlined and automated
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over time. For the time being, please use the following process to add new
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wheels:
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1. Install `Starforge`_ (e.g. with ``pip install starforge`` or ``python
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setup.py install`` from the source). You will also need to have Docker
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installed on your system.
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2. Obtain `wheels.yml`_ (this file will most likely be moved in to Galaxy in
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the future) and add/modify the wheel definition.
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3. Use ``starforge wheel --wheels-config=wheels.yml <wheel-name>`` to build the
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wheel. If the wheel includes C extensions, you will probably want to also
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use the ``--no-qemu`` flag to prevent Starforge from attempting to build on
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Mac OS X using QEMU/KVM.
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4. If the wheel build is successful, submit a pull request to `Starforge`_ with
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your changes to `wheels.yml`_.
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5. A `Galaxy Committers group`_ member will need to trigger an automated build
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of the wheel changes in your pull request. Galaxy's Jenkins_ service will
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build these changes using Starforge.
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6. If the pull request is merged, submit a pull request to Galaxy modifying the
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files in `lib/galaxy/dependencies`_ as appropriate.
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You may attempt to skip directly to step 4 and let the Starforge wheel PR
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builder build your wheels for you. This is especially useful if you are simply
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updating an existing wheel's version. However, if you are adding a new C
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extension wheel that is not simple to build, you may need to go through many
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iterations of updating the PR and having a `Galaxy Committers group`_ member
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triggering builds before wheels are successfully built. You can avoid this
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cycle by performing steps 1-3 locally.
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.. _Starforge:
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.. _Galaxy Starforge: https://github.com/galaxyproject/starforge/
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.. _wheels.yml: https://github.com/galaxyproject/starforge/blob/master/wheels/build/wheels.yml
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.. _Galaxy Committers group: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organization.rst#committers
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.. _Jenkins: https://jenkins.galaxyproject.org/
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.. _lib/galaxy/dependencies: https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/dependencies
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@@ -26,6 +26,10 @@ Highlights
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Work done as part of this to enable binary dependencies on Linux has been
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included with the recently released pip_ 8.
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Detailed documentation on these changes and their impact under a variety of
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Galaxy deployment scenarios can be found in the :ref:`framework-dependencies`
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section of the Admin documentation.
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**Nested Workflows**
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Workflows may now run other workflows as a single abstract step in the parent
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workflow. This allows for reusing or subworkflows in your analyses.
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