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 is Python 3 compatible.
Free software: Academic Free License version 3.0
Documentation: https://galaxy-lib.readthedocs.org.
History
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 galaxy.tools.toolbox (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 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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