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Subset of Galaxy ( core code base designed to be used a library.

Project description

Documentation Status


A small subset of the Galaxy project for reuse outside the core. This subset has minimal dependencies and is Python 3 compatible.


19.5.2 (2019-04-28)

  • Update to latest Miniconda version.

19.5.1 (2019-03-03)

  • Fix API method interface change breaking Planemo compatibility.

19.5.0 (2019-03-01)

  • Synchronize with the development tip of Galaxy.
  • Fix Travis CI configuration (thanks to @nsoranzo).

18.9.2 (2019-01-02)

  • Implement option for uploading local test data.
  • Bring in the latest Galaxy changes, which provide Python 3.7 support.

18.9.1 (2018-09-15)

  • More work improving channel handling for mulled containers.

18.9.0 (2018-09-14)

  • Update Conda channel order (thanks to @bgruening).
  • Bring in the latest Galaxy changes and add Galaxy XSD to the project.
  • Various cwltool fixes (thanks to @nsoranzo).

18.5.15 (2018-09-12)

  • More tweaks to CWL tool loading to support newer versions of cwltool.

18.5.14 (2018-09-12)

  • Improved tool linting and reporting thanks to @natefoo and @nsoranzo.
  • Add support for newer cwltool thanks to @nsoranzo.
  • Improved mulled building thanks to @pcm32.

18.5.13 (2018-05-23)

  • Small updates to test parsing to support Galaxy workflow testing.

18.5.12 (2018-05-22)

  • Update test data processing to allow URIs in Galaxy workflow tests.

18.5.11 (2018-05-16)

  • Parse CWL SoftwareRequirements to Galaxy requirements (required to fix various Planemo functionality for CWL tools).

18.5.10 (2018-05-10)

  • Docker logging API fix for Planemo.

18.5.9 (2018-05-07)

  • Update CWL linting to target CWL 1.0.

18.5.8 (2018-05-06)

  • Better error handling for Conda searching (thanks to @bgruening).
  • Update against the latest Galaxy codebase.
  • Add Galaxy tool linting to ensure versions are PEP 440 compliant (thanks to @davebx).

18.5.7 (2018-03-12)

  • More tool testing client fixes, this time for ephemeris.

18.5.6 (2018-03-12)

  • Bring in the latest Galaxy dev branch - includes code cleanup and many Python 3 fixes from @nsoranzo as well as client code for executing tool tests against external Galaxy instances.
  • Extend tool testing client from Galaxy’s dev branch with even more data collection for compatiblity with Planemo.

18.5.5 (2018-03-06)

  • Fix mulled to use shlex.quote to escape single quotes in test command (thanks to @mbargull).
  • Make markupsafe a dependency since it is import unconditionally in (thanks to @mbargull).
  • Python 3 fix for assertion testing.

18.5.4 (2018-03-01)

  • Make conda image for mulled builds configurable via an environment variable (thanks to @mbargull).

18.5.3 (2018-02-28)

  • Fix path module for import on Windows for Pulsar.

18.5.2 (2018-02-28)

  • Various fixes for library usage mostly related to Conda (with help from @nsoranzo).

18.5.1 (2018-02-26)

  • Redo last release - pushed to PyPI without actually including the desired fix.

18.5.0 (2018-02-26)

  • Another Python 3 fix for Planemo.
  • Fix galaxy-lib version - this has actually been tracking the 18.05 release of Galaxy for the last two releases.

18.1.0 (2018-02-26)

  • More Python 3 fixes for Planemo thanks to @nsoranzo.
  • Bring in the latest Galaxy development branch.

17.9.12 (2018-02-22)

  • Python 3 fix for Planemo thanks to @nsoranzo.
  • Fix bad merge of miniconda update for mulled work.

17.9.11 (2018-02-22)

  • Update to the latest Galaxy dev just prior to the branch of 18.01.
  • Python 3 fixes.

17.9.10 (2017-11-23)

  • Added docs for using mulled-build with your own account (thanks to @jerowe).
  • Catch errors in Conda search if nothing is found (preventing planemo-monitor from functioning properly) (thanks to @bgruening).
  • Make multi-requirement container building via mulled more stable (thanks to @bgruening).

17.9.9 (2017-09-27)

  • Bring in latest updates from the 17.09 branch of Galaxy - including updating the default target Conda version and fixes for module resolution.

17.9.8 (2017-09-26)

  • Bring in updated CWL utilities from the upstream work on CWL integration.

17.9.7 (2017-09-19)

  • Bring in updated CWL utilities from the upstream work on CWL integration.

17.9.6 (2017-09-15)

  • Remove command lint check that is no longer valid.

17.9.5 (2017-09-06)

  • Bring in updated CWL utilities from the upstream work on CWL integration.

17.9.4 (2017-09-06)

  • Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo).
  • Improved error handling when parsing tool reStructuredText (thanks to @erasche).
  • Updated CWL utilities.

17.9.3 (2017-06-27)

  • Bug fix in from_dict parsing of tool dependency specs.

17.9.2 (2017-06-22)

  • Sync with mulled enhancements and fixes from Galaxy’s development branch.

17.9.1 (2017-06-17)

  • Various small Singularity fixes and enhancements.

17.9.0 (2017-06-11)

  • Bring in latest Galaxy dev changes.
  • Implement support for building Singularity mulled containers.
  • Implement mulled version 2 package hashing.
  • Fix default namespace for mulled operations from mulled to biocontainers.

17.5.11 (2017-05-31)

  • Fix HISTORY.rst formatting to properly render release on PyPI.
  • Fix bug in new offline Conda search function introduced in 17.5.10.

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 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 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 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 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 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 package in
  • 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.

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