Fix essentially all Conda and BioContainers related functionality to allow parity between
CWL and existing Galaxy functionality - fixes and enhances many commands including lint,
conda_install, conda_env, test, run, and mull.
Pull Request 828
Add two new tutorials for Conda
development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
CWL exercises, answers, and example project templates.
Improve the CWL generated by the tool_init command to properly deal with
SoftwareRequirement s and generate more idiomatic CWL.
Pull Request 820, a5c72e3
Add new engine type (--engine toil) for testing and running CWL tools (requires
manually installing Toil with pip install toil in Planemo's environment).
Pull Request 831
Change behavior of --docker flag, for a few releases it would require
Galaxy use a container for every non-upload tool. This breaks various
conversion tools for instance and so was reverted.
Pull Request 733
Implement an open (or just o) command to quickly open the last test results
(or any file if supplied). Pull Request 641
Linting improvements and fixes due to galaxy-lib update.
* WARN on test output names not found or not matching.
* INFO correct information about stdio if profile version is found.
* WARN if profile version is incorrect.
* INFO profile version
* Fix assert_command not detected as a valid test (fixes Issue 260).
Have lint --conda_requirements check that at least one actual requirement is found.
Allow conda_install to work with packages as well as just tools.
Add --global option to conda_install to install requirements into global Conda setup
instead of using an environment.
Implement planemo lint --biocontainer that checks that a tool has an available BioContainer
Add more options and more documentation to the planemo mull command.
Hack around a bug in Conda 4.2 that makes it so planemo mull doesn't work out of the box on
Mac OS X.
Allow URIs to be used instead of paths for a couple operations. ce0dc4e
Update to the latest galaxy-lib release. This means new installs start with
Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
Conda related bugs.
Change defaults so that Conda automatically initializes and performs tool installs
by default from within the spawned Galaxy server. The trio of flags
--conda_dependency_resolution, --conda_auto_install, and --conda_auto_init
are effectively enabled by default now. 4595953
Implement mull command to build containers for tools based on Conda
recipes matching requirement definitions. 08cef54
Implement --mulled_containers flag on test, serve, and run
commands to run tools in "mulled" containers. Galaxy will first search
locally cache containers (such as ones built with mull), then search
the mulled namespace of quay.io, and finally build one on-demand if
needed using galaxy-lib and Involucro developed by @thriqon.
Implement --conda_requirements flag on lint command to ensure requirements
can be resolved in best practice channels. 9da8387
Allow conda_install command over multiple tool paths. 2e4e5fc
Update pip as part of setting virtual environment in Makefile target.
Add script to auto-update Bioconda recipe for Planemo and open a pull request.
Fix HISTORY.rst link problem that prevented correct display of content on PyPI.
Implement Engine and Runnable abstractions - Planemo now has
beta support for testing Galaxy workflows and CWL tools with Galaxy and
any CWL artifact with cwltool.
Pull Request 454, 7be1bf5
Fix missing command_line in test output json. e38c436
More explicit Galaxy job_conf.xml handling, fixes bugs caused by
galaxy_root having existing and incompatible job_conf.xml files
and makes it possible to specify defaults with fixed server name. c4dfd55
Introduce profile commands (profile_create, profile_delete, and
profile_list) and profile improvements (automatic postgres database
creation support). Pull Request 480, a87899b
Rework Galaxy test reporting to use structured data instead of XUnit
Refactor Galaxy configuration toward support for running Galaxy in
docker-galaxy-stable. Pull Request 479
Implement Galaxy "profiles" - the ability to configure
perisistent, named environments for serve and test.
Greatly improved serve command - make test-data
available as an FTP folder, (on 16.07) automatically log
in an admin user, and many more options (such as those
required for "profiles" and a --daemon mode).
Add documentation on GALAXY_SLOTS and running planemo
on a cluster. 45135ff, e0acf91
Revise command-line handling framework for consistency and
extension - allow extra options to be configured as
defaults ~/.planemo.yml including --job_config_file
and Conda configuration options. e769118, 26e378e
Fix tool_init commans options typos (thanks to
Nitesh Turaga). 826d371
Refactor galaxy-related modules into submodules of a new
planemo.galaxy package. 8e96864
Implement smarter shed_diff command - it now produces a meaningful
exit codes and doesn't report differences if these correspond to attributes
that will be automatically populated by the Tool Shed. Issue 167
Use new smarter shed_diff code to implement a new --check_diff
option for shed_upload - to check for meaningful differences before
updating repositories. Issue 168
Record git commit hash during shed_upload if the .shed.yml is
located in a git repository. Issue 170
Allow shed_ operations to operate on git URLs directly. Issue 169
Fail if missing file inclusion statements encountered during .shed.yml
repository resolution - bug reported by @peterjc. Issue 158
Improved exception handling for tool shed operations including new
--fail_fast command-line option. * Issue 114, Pull Request 173
Implement more validation when using the shed_init command. 1cd0e2d
Add -r/--recursive option to shed_download and shed_diff
commands and allow these commands to work with .shed.yml files defining
multipe repositories. 40a1f57
Add --port option to the serve and tool_factory commands.
Fix unnessecary lint warning about parallelism tag reported by
Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
Implement the new shed_lint command that verifies various aspects of tool
shed repositories - including XSD validation of repository_dependencies.xml
and tool_dependencies.xml files, best practices for README files, and the
contents of .shed.yml files. This requires the lxml library to be available
to Planemo or the application xmllint to be on its PATH. Pull Request 130Issue 89Issue 91912df02d26929e36ac6d8
Allow skipping specific linters when using the lint command using the new
--skip option. 26e3cdb
Implement sophisticated options in .shed.yml to map a directory to many,
custom Tool Shed repositories during shed operaitons such shed_upload
including automatically mapping tools to their own directories and automatically
building suites repositories. Pull Request 143
Make shed_upload more intelligent when building tar files so that package
and suite repositories may have README files in source control and they will
just be filtered out during upload. 53edd99
Implement a new shed_init command that will help bootstrap .shed.yml
files in the specified directory. cc1a447
Extend shed_init to automatically build a repository_rependencies.xml
file corresponding to a Galaxy workflow (.ga file). Issue 118988de1d
In addition to a single file or directory, allow lint to be passed multiple
files. 343902dIssue 139
Add -r/--recursive option to shed_create and lint commands. 63cd43101f2af9
Improved output formatting and option to write diffs to a file for the
shed_diff command. 965511d
Fix lint problem when using new Galaxy testing features such as expecting
job failures and verifing job output. Issue 138
Grab updated test database to speed up testing (thanks to approach from
E. Rasche and Dannon Baker). Issue 61, dff4f33
Fix test data command-line argument name (was test-data now it is
Use tool_data_table_conf.xml.sample file if
tool_data_table_conf.xml.test is unavailable. Should allow some
new tools to be tested without modifying Galaxy's global
tool_data_table_conf.xml file. ac4f828
Improvements to way Planemo loads its own copy of Galaxy modules to prevent
various conflicts when launching Galaxy from Planemo. Pull Request 56
Allow setting various test output options in ~/.planemo.yml and disabling
JSON output. 21bb463
More experimental Brew and Tool Shed options that should not be considered
part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
Fix project_init for BSD tar (thanks to Nitesh Turaga for the bug
Documentation fixes for tool linting command (thanks to Nicola Soranzo).
Pull Request 51