Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library.
Project description
Overview
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.
History
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 quay.io 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Remove command lint check that is no longer valid.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 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.
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