galaxy-lib 17.5.10

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A small subset of the Galaxy_ project for reuse outside the core. This subset has minimal dependencies and should be Python 3 compatible.

* Free software: Academic Free License version 3.0
* Documentation: https://galaxy-lib.readthedocs.org.
* Code: https://github.com/galaxyproject/galaxy-lib


.. _Galaxy: http://galaxyproject.org/
.. _GitHub: https://github.com/
.. _Docker: https://www.docker.com/
.. _Homebrew: http://brew.sh/
.. _linuxbrew: https://github.com/Homebrew/linuxbrew
.. _Vagrant: https://www.vagrantup.com/
.. _Travis CI: http://travis-ci.org/
.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
.. _Common Workfow Language: http://common-workflow-language.github.io




History
-------

.. to_doc

---------------------
17.5.10 (2017-05-30)
---------------------

* Always clean up build directory in mulled commands (thanks to @johanneskoester).
* Expose offline mode in Conda search utility (for repeated fast searches).
* When publishing mulled containers - use quay.io API to publish them as public.
* Add explicit option ``--check-published`` to mulled-build-*.
* Fix auto-installation of Involucro on first attempt.
* Handle explicit tags in ``mulled-build-files`` and add an implicit tag of ``0`` if none found.
* Fix tab parsing in ``mulled-build-files``.

---------------------
17.5.9 (2017-05-16)
---------------------

* Make mulled-search to search biocontainers instead of mulled repository by default
(thanks to @tom-tan).
* Allow setting a new base image with mulled-build.

---------------------
17.5.8 (2017-04-23)
---------------------

* Fix mulled image cleanup. #55.

---------------------
17.5.7 (2017-03-15)
---------------------

* Updates to CWL library functionality for several months worth of CWL tool updates.
* Allow finding tools by a URI-like strings (e.g. ``file://``, ``http://``, ``dockstore://``).
* Bring in latest Galaxy updates.

---------------------
17.5.6 (2017-03-01)
---------------------

* Expanded options for mulled CLI tools and library functionality.
Fixes #49.

---------------------
17.5.5 (2017-02-26)
---------------------

* Fix bug in 17.5.4 where under certain conditions conda-build would attempt to be setup
with the conda --use-local flag - which is not allowed.

---------------------
17.5.4 (2017-02-26)
---------------------

* Fix local builds Conda support to reflect conda-build is required.
* Fix default target path for miniconda installs.

---------------------
17.5.3 (2017-02-24)
---------------------

* Update against the latest Galaxy dev branch changes.
* Update Conda utilities to allow using locally built packages.

---------------------
17.5.2 (2017-02-21)
---------------------

* Conda utility enhancements to fix a Planemo bug.

---------------------
17.5.1 (2017-02-21)
---------------------

* Various improvements to Galaxy tool linting.

---------------------
17.5.0 (2017-02-16)
---------------------

* Bring in the last of the Galaxy dev changes.
* Allow Conda installs to target global Conda config (for Planemo)

---------------------
17.1.2 (2017-01-23)
---------------------

* Bring in the last of the Galaxy dev changes before branch of release_17.01.
* Improvements to mulled testing thanks to @mvdbeek.

---------------------
17.1.1 (2016-12-14)
---------------------

* Revert changes to shell command execution in Galaxy that had unintended consequences for Planemo.

---------------------
17.1.0 (2016-12-12)
---------------------

* Improved mulled logging thanks to @bgruening.
* Bring in the latest Galaxy dev changes.

---------------------
16.10.10 (2016-10-24)
---------------------

* Fix mulled package data fetching for Mac OS X (thanks to @dannon).

---------------------
16.10.9 (2016-10-21)
---------------------

* Small fixes including to reflect mulled name on quay.io changed to biocontainers.

---------------------
16.10.8 (2016-10-10)
---------------------

* More mulled enhancements and bug fixes thanks to @bgruening and @daler.

---------------------
16.10.7 (2016-10-08)
---------------------

* More mulled enhancements and bug fixes thanks to @bgruening.
* Fix bioconda support by adding conda-forge to list of default channels.

---------------------
16.10.6 (2016-10-07)
---------------------

* More mulled enhancements thanks to @bgruening.

---------------------
16.10.5 (2016-10-04)
---------------------

* Some docstring cleanup and minor tweaks to Conda support for downstream planemo mulled work.

---------------------
16.10.4 (2016-10-03)
---------------------

* More mulled fixes and enhancements.

---------------------
16.10.3 (2016-10-02)
---------------------

* Small mulled and Conda related fix and enhancements.

---------------------
16.10.2 (2016-09-30)
---------------------

* Fix setup.py for features in 16.10.1.

---------------------
16.10.1 (2016-09-29)
---------------------

* Updates for recents changes to Galaxy and initial mulled scripts and container resolver.

---------------------
16.10.0 (2016-08-31)
---------------------

* Updates for recent changes to Galaxy.

---------------------
16.7.10 (2016-08-04)
---------------------

* Updates for recent change to Galaxy.

---------------------
16.7.9 (2016-06-13)
---------------------

* Updates for recent changes to Galaxy and cwltool.

---------------------
16.7.8 (2016-06-05)
---------------------

* Updates to include Galaxy library for verifying test outputs
and the latest dev changes to Galaxy.

---------------------
16.7.7 (2016-05-23)
---------------------

* Fixes to CWL and Docker libraries for Planemo.

---------------------
16.7.6 (2016-05-11)
---------------------

* Fixes to cwl processing for Planemo.

---------------------
16.7.5 (2016-05-11)
---------------------

* Updates to cwl processing for Planemo.

---------------------
16.7.4 (2016-05-10)
---------------------

* Updates to cwl processing for Planemo.

---------------------
16.7.3 (2016-05-07)
---------------------

* Updates to cwltool_deps for Planemo.

---------------------
16.7.2 (2016-05-06)
---------------------

* Updates to tool parsing and linting for Planemo.

---------------------
16.7.1 (2016-05-02)
---------------------

* Update against the latest development branch of Galaxy.

---------------------
16.7.0 (2016-04-21)
---------------------

* Update against the latest development branch of Galaxy.

---------------------
16.4.1 (2016-04-08)
---------------------

* Update against the latest development branch of Galaxy.

---------------------
16.4.0 (2016-02-15)
---------------------

* Update against the latest development branch of Galaxy.

---------------------
16.1.9 (2016-01-14)
---------------------

* Fix a bug in the source distribution of galaxy-lib.

---------------------
16.1.8 (2016-01-12)
---------------------

* Update against Galaxy's release_16.01 branch.

---------------------
16.1.7 (2016-01-03)
---------------------

* Update against Galaxy's dev branch - including conda updates,
dependency resolution changes, and toolbox updates.

---------------------
16.1.6 (2015-12-28)
---------------------

* Additional fixes to setup.py and updates for recent changes to
Galaxy's dev branch.

---------------------
16.1.5 (2015-12-22)
---------------------

* Fix another bug that was preventing dependency resolution from
working in Pulsar.

---------------------
16.1.4 (2015-12-22)
---------------------

* Another setup.py fix for job metrics module.

---------------------
16.1.3 (2015-12-22)
---------------------

* Python 3 fixes and updates for recent Galaxy dev commits.

---------------------
16.1.2 (2015-12-21)
---------------------

* Fix for missing galaxy.tools.parser package in setup.py.
* Fix LICENSE in repository.

---------------------
16.1.1 (2015-12-20)
---------------------

* Fix small issues with dependencies, naming, and versioning with first release.

---------------------
16.1.0 (2015-12-20)
---------------------

* Setup project.

.. _bioblend: https://github.com/galaxyproject/bioblend/
.. _XSD: http://www.w3schools.com/schema/
.. _lxml: http://lxml.de/
.. _xmllint: http://xmlsoft.org/xmllint.html
.. _nose: https://nose.readthedocs.org/en/latest/