Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5a276ec3e69de63dc574759db59cd083c1b80b8b
https://github.com/galaxyproject/galaxy/commit/5a276ec3e69de63dc574759db59c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-model.js
A client/galaxy/scripts/mvc/library/library-util.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-model.js.map
A static/maps/mvc/library/library-util.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-model.js
A static/scripts/mvc/library/library-util.js
Log Message:
-----------
start work on new lirbary comparators
Commit: 987f016246ebb5e7474c3e5f2bedeb38a8786e0e
https://github.com/galaxyproject/galaxy/commit/987f016246ebb5e7474c3e5f2bed…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-util.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-util.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-util.js
Log Message:
-----------
rework the comparator to work when key is missing from object
Commit: 8bde43214cbca1eb31958b4280e1bda93b43fd3a
https://github.com/galaxyproject/galaxy/commit/8bde43214cbca1eb31958b4280e1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
Log Message:
-----------
remove forgotten comment
Commit: c41225b422662a29aa7a43922beac2ffafd2a81b
https://github.com/galaxyproject/galaxy/commit/c41225b422662a29aa7a43922bea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-util.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-util.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-util.js
Log Message:
-----------
datalibs add func to sort folder by desc/state
refactor the comparator a bit to not change the actual obejcts' prperties
Commit: be4ddd3cd0acdd1d8049f23fbaff577447aaf78f
https://github.com/galaxyproject/galaxy/commit/be4ddd3cd0acdd1d8049f23fbaff…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M .travis.yml
M Makefile
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/style/less/base.less
M client/gulpfile.js
M client/package.json
M client/yarn.lock
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M doc/schema_template.md
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/path/ntpath.py
M run_tests.sh
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/style/blue/base.css
M test/api/test_tools.py
A test/functional/tools/data_source.py
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/test_data_source.xml
M test/qunit/Gruntfile.js
M test/qunit/package.json
M test/qunit/test-app.js
M test/qunit/test-common.js
R test/qunit/test-libs/qunit-1.23.1.css
R test/qunit/test-libs/qunit-1.23.1.js
R test/qunit/test-libs/sinon-1.17.7.js
R test/qunit/test-libs/sinon-qunit-1.0.0.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/graph.js
M test/qunit/tests/hda-base.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/job-dag.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/popover_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/utils_test.js
M test/qunit/tests/workflow_editor_tests.js
M tox.ini
Log Message:
-----------
Merge branch 'dev' into lib-comparators
Commit: 81a2163c87c28ae3ba4a3d4114a0c7e1c28441c6
https://github.com/galaxyproject/galaxy/commit/81a2163c87c28ae3ba4a3d4114a0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
repack
Commit: 62637405b591b8b9dc1d061bd7d19055cb363c8d
https://github.com/galaxyproject/galaxy/commit/62637405b591b8b9dc1d061bd7d1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-30 (Mon, 30 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-model.js
A client/galaxy/scripts/mvc/library/library-util.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-model.js.map
A static/maps/mvc/library/library-util.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-model.js
A static/scripts/mvc/library/library-util.js
Log Message:
-----------
Merge pull request #4877 from martenson/lib-comparators
add sorting options for data library folders
Compare: https://github.com/galaxyproject/galaxy/compare/9257e93faf9b...62637405b591
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c9799013ee910d74a8d1953275822305ab128749
https://github.com/galaxyproject/galaxy/commit/c9799013ee910d74a8d195327582…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Updates and enhancements for the Docker testing Dockerfile.
- Target dev on Github instead of stable on bitbucket for base dependencies and migrations.
- Update to Ubuntu 16.04 ahead of trying to merge in Selenium support (should be a bit slimmer without the TS requirements layer also).
- Use fancy new Node compatible with yarn.
Commit: 9257e93faf9bc5cc8c96d1e07afce9614897d5ec
https://github.com/galaxyproject/galaxy/commit/9257e93faf9bc5cc8c96d1e07afc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Merge pull request #4885 from jmchilton/testing_dockerfile_0
Updates and enhancements for the testing Dockerfile.
Compare: https://github.com/galaxyproject/galaxy/compare/235a590b69e4...9257e93faf9b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5e584bbe5557b265f1c4f1bfe8386239678032e5
https://github.com/galaxyproject/galaxy/commit/5e584bbe5557b265f1c4f1bfe838…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Update various Galaxy requirements.
At least requests and Babel are required to get the latest "locked" version of the dev requirements compatible with our current locked versions in requirements.txt.
Removed repoze.lru from an earlier variant of this since the wheel didn't work - good catch @nsoranzo.
Commit: 235a590b69e431cf6f060da004834ae482e607de
https://github.com/galaxyproject/galaxy/commit/235a590b69e431cf6f060da00483…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #4884 from jmchilton/update_babel
Update various Galaxy requirements.
Compare: https://github.com/galaxyproject/galaxy/compare/64cf2946f2c0...235a590b69e4
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: aef5f4fa95c56362029dba6cf636103cf235fd13
https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
[16.10] Fix test fixtures dependency.
It should have never been in the pinned requirements and has disappeared from PyPI.
Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483
https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-27 (Fri, 27 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #4873 from jmchilton/fix_test_fixtures
[16.10] Fix test fixtures dependency.
Compare: https://github.com/galaxyproject/galaxy/compare/90289b6116c6...7bf2bbfa4050
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7b9cd447004daedca6e18b4e97a67fce8c0667e0
https://github.com/galaxyproject/galaxy/commit/7b9cd447004daedca6e18b4e97a6…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-18 (Wed, 18 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
A config/plugins/tours/test.yaml
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Added tour groups for more clarity if there are a lot of tours.
Commit: d9045deea69e74590d079b05a1bec02e29a6aa18
https://github.com/galaxyproject/galaxy/commit/d9045deea69e74590d079b05a1be…
Author: selten <selten(a)users.noreply.github.com>
Date: 2017-10-18 (Wed, 18 Oct 2017)
Changed paths:
R config/plugins/tours/test.yaml
Log Message:
-----------
Delete test.yaml
Accidentally added file to GIT for design checking.
Commit: dea036f66a790444a3aae473617bf48d4a1b4827
https://github.com/galaxyproject/galaxy/commit/dea036f66a790444a3aae473617b…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-19 (Thu, 19 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Use tags instead of groups
Commit: 49b9543b77a1419e1bfd13d502239d9c35fe2a1e
https://github.com/galaxyproject/galaxy/commit/49b9543b77a1419e1bfd13d50223…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-19 (Thu, 19 Oct 2017)
Changed paths:
R config/plugins/tours/test.yaml
Log Message:
-----------
Merge remote-tracking branch 'origin/dev' into dev
Commit: 19445547298d9b9405965cf83a928cc8afaeccf4
https://github.com/galaxyproject/galaxy/commit/19445547298d9b9405965cf83a92…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-19 (Thu, 19 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Added hiding of tags.
Commit: 75117e407e0b03ee2537cd029b8fbbc345c1e7a6
https://github.com/galaxyproject/galaxy/commit/75117e407e0b03ee2537cd029b8f…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-19 (Thu, 19 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Make sure description is still shown
Commit: a3c00c122c02d3b183c90da83818005fadafda86
https://github.com/galaxyproject/galaxy/commit/a3c00c122c02d3b183c90da83818…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-19 (Thu, 19 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M config/datatypes_conf.xml.sample
M config/plugins/webhooks/demo/tour_generator/static/script.js
A lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/util/__init__.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M static/maps/mvc/form/form-parameters.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Commit: 4dc97ceb5950ee1bda5c2de2a9e569a7fab2735b
https://github.com/galaxyproject/galaxy/commit/4dc97ceb5950ee1bda5c2de2a9e5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Build client/formatting.
Commit: b777762524ea856962ec3c1c13baa140e9fab766
https://github.com/galaxyproject/galaxy/commit/b777762524ea856962ec3c1c13ba…
Author: selten <selten(a)users.noreply.github.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Merge pull request #1 from dannon/selten_dev
Build client/formatting.
Commit: 4fcf2a329f66e29c16898d0c4897f49f20e0fd9a
https://github.com/galaxyproject/galaxy/commit/4fcf2a329f66e29c16898d0c4897…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Untagged tour support/rendering.
Commit: df1b7fbf548ad5ffd85b127eb12a3fbead82b7d2
https://github.com/galaxyproject/galaxy/commit/df1b7fbf548ad5ffd85b127eb12a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Capitalize tag rendering
Commit: 7d1a8d8553765ef72da7c8e500a6ca31647d2ab9
https://github.com/galaxyproject/galaxy/commit/7d1a8d8553765ef72da7c8e500a6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M config/plugins/tours/core.scratchbook.yaml
Log Message:
-----------
Minor typo, consistent use of form for 'visualization/visualisation'
Commit: 3138e025366dd088a184d952e76cf5e748077711
https://github.com/galaxyproject/galaxy/commit/3138e025366dd088a184d952e76c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/style/less/base.less
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/style/blue/base.css
Log Message:
-----------
Add a little bit of padding between labels.
Commit: f5ae8d26fee5c74fff827cba10fda2b516577353
https://github.com/galaxyproject/galaxy/commit/f5ae8d26fee5c74fff827cba10fd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
Log Message:
-----------
Swap from default to 'core' to be consistent with the namespace of the file.
Commit: 32ffcaf990037db4ca58c0071f6aed48bd3abb13
https://github.com/galaxyproject/galaxy/commit/32ffcaf990037db4ca58c0071f6a…
Author: selten <selten(a)users.noreply.github.com>
Date: 2017-10-24 (Tue, 24 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/style/less/base.less
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #2 from dannon/selten_dev
A few more tweaks to tours
Commit: b3866bae1623cd8c67cee8fd787fc823e1da31c9
https://github.com/galaxyproject/galaxy/commit/b3866bae1623cd8c67cee8fd787f…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/torque.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/image_util.py
M lib/galaxy/util/object_wrapper.py
A lib/galaxy/util/path/__init__.py
A lib/galaxy/util/path/ntpath.py
A lib/galaxy/util/path/posixpath.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
R lib/galaxy/webapps/galaxy/controllers/external_service.py
R lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/request_type.py
R lib/galaxy/webapps/galaxy/controllers/requests.py
R lib/galaxy/webapps/galaxy/controllers/requests_admin.py
R lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/psyco_full.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/drmaa_external_runner.py
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/rst2html.py
M scripts/runtime_stats.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M setup.cfg
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/libs/backbone.js.map
M static/maps/libs/bibtex.js.map
M static/maps/libs/d3.js.map
A static/maps/libs/jquery/jquery.complexify.js.map
M static/maps/libs/jquery/jquery.cookie.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/jquery/jquery.mousewheel.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/underscore.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/style/blue/library.css
R templates/admin/external_service/common.mako
R templates/admin/external_service/create_external_service.mako
R templates/admin/external_service/edit_external_service.mako
R templates/admin/external_service/grid.mako
R templates/admin/external_service/reload_external_service_types.mako
R templates/admin/external_service/view_external_service.mako
R templates/admin/request_type/common.mako
R templates/admin/request_type/create_request_type.mako
R templates/admin/request_type/edit_request_type.mako
R templates/admin/request_type/grid.mako
R templates/admin/request_type/request_type_permissions.mako
R templates/admin/request_type/view_request_type.mako
R templates/admin/requests/grid.mako
R templates/admin/requests/reject.mako
R templates/admin/requests/rename_datasets.mako
R templates/admin/requests/sample_datasets_grid.mako
R templates/admin/requests/view_sample_dataset.mako
R templates/admin/tool_shed_repository/repair_repository.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/requests/common/add_samples.mako
R templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/requests/common/create_request.mako
R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako
R templates/webapps/galaxy/requests/common/edit_samples.mako
R templates/webapps/galaxy/requests/common/find_samples.mako
R templates/webapps/galaxy/requests/common/index.mako
R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako
R templates/webapps/galaxy/requests/common/sample_datasets.mako
R templates/webapps/galaxy/requests/common/sample_state.mako
R templates/webapps/galaxy/requests/common/view_request.mako
R templates/webapps/galaxy/requests/common/view_request_history.mako
R templates/webapps/galaxy/requests/common/view_sample.mako
R templates/webapps/galaxy/requests/common/view_sample_datasets.mako
R templates/webapps/galaxy/requests/common/view_sample_history.mako
R templates/webapps/galaxy/requests/find_samples_index.mako
R templates/webapps/galaxy/requests/grid.mako
R templates/webapps/galaxy/requests/index.mako
M test/base/testcase.py
M test/functional/twilltestcase.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
M test/unit/managers/test_UserManager.py
M test/unit/tools/test_tool_deps.py
M tools/data_source/data_source.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/genomespace/genomespace_importer.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Ensure Galaxy doesn't crash when a tour is malformed.
Commit: 89e843730e23ee46a6152a4683f37d99d1251cc0
https://github.com/galaxyproject/galaxy/commit/89e843730e23ee46a6152a4683f3…
Author: Peter Selten <peter.selten98(a)gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Ensure galaxy can boot even with a malformed tour.
Commit: 7b3235a71cc229988a3641c27a8d05712aa8171f
https://github.com/galaxyproject/galaxy/commit/7b3235a71cc229988a3641c27a8d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Rebuild client.
Commit: de9f8a6094f0bc4eac9b038c0ba9efdfbd0c61bc
https://github.com/galaxyproject/galaxy/commit/de9f8a6094f0bc4eac9b038c0ba9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/style/less/base.less
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M lib/galaxy/tours/__init__.py
M static/maps/mvc/tours.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'selten/dev' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/862212ad40f4...de9f8a6094f0
Branch: refs/heads/galaxyenv
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: fe919ae973e1c6a2b9c777624ff4b44a2ddef969
https://github.com/galaxyproject/infrastructure-playbook/commit/fe919ae973e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
A env/galaxy/files/apache/galaxy-installers.conf
A env/galaxy/files/jenkins/jenkins_server_user_ssh_config
A env/galaxy/files/jenkins/jenkins_slave_user_ssh_config
A env/galaxy/files/orval/rsyncd.xml
A env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem
A env/galaxy/files/ssl/wildcard_cert.pem
A env/galaxy/group_vars/all.yml
A env/galaxy/group_vars/baseenv.yml
A env/galaxy/group_vars/cvmfsstratum0servers.yml
A env/galaxy/group_vars/cvmfsstratum1servers.yml
A env/galaxy/group_vars/ec2hosts.yml
A env/galaxy/group_vars/jenkinsservers.yml
A env/galaxy/group_vars/jenkinsslaves.yml
A env/galaxy/group_vars/listservers.yml
A env/galaxy/group_vars/liteenv.yml
A env/galaxy/group_vars/mailservers.yml
A env/galaxy/group_vars/starforgebuilders.yml
A env/galaxy/host_vars/athena.galaxyproject.org.yml
A env/galaxy/host_vars/chouffe.galaxyproject.org.yml
A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org.yml
A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org.yml
A env/galaxy/host_vars/cvmfs1-iu0.galaxyproject.org.yml
A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org.yml
A env/galaxy/host_vars/cvmfs1-tacc0.galaxyproject.org.yml
A env/galaxy/host_vars/delirium.galaxyproject.org.yml
A env/galaxy/host_vars/duvel.galaxyproject.org.yml
A env/galaxy/host_vars/jetstream-iu0.galaxyproject.org.yml
A env/galaxy/host_vars/jetstream-tacc0.galaxyproject.org.yml
A env/galaxy/host_vars/leeroy.galaxyproject.org.yml
A env/galaxy/host_vars/n4.galaxyproject.org.yml
A env/galaxy/host_vars/n6.galaxyproject.org.yml
A env/galaxy/host_vars/orval.galaxyproject.org.yml
A env/galaxy/host_vars/westvleteren.galaxyproject.org.yml
A env/galaxy/inventory
A env/galaxy/library/README
A env/galaxy/library/cron.py
A env/galaxy/playbook.yml
A env/galaxy/secret_group_vars/all.yml
A env/galaxy/secret_group_vars/dockersslservers.yml
A env/galaxy/secret_group_vars/dockerswarmmanagers.yml
A env/galaxy/secret_group_vars/jenkinsslaves.yml
A env/galaxy/secret_group_vars/sslwebservers.yml
A env/galaxy/secret_host_vars/athena.galaxyproject.org.yml
A env/galaxy/secret_host_vars/biostar.usegalaxy.org.yml
A env/galaxy/secret_host_vars/chouffe.galaxyproject.org.yml
A env/galaxy/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/default.yml
A env/galaxy/secret_host_vars/delirium.galaxyproject.org.yml
A env/galaxy/secret_host_vars/leeroy.galaxyproject.org.yml
A env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml
A env/galaxy/secret_host_vars/orval.galaxyproject.org.yml
A env/galaxy/secret_host_vars/radegast.galaxyproject.org.yml
A env/galaxy/secret_host_vars/westvleteren.galaxyproject.org.yml
A env/galaxy/templates/nginx/bioarchive.j2
A env/galaxy/templates/nginx/cloudlaunch.j2
A env/galaxy/templates/nginx/depot.j2
A env/galaxy/templates/nginx/docs.j2
A env/galaxy/templates/nginx/duvel.j2
A env/galaxy/templates/nginx/eggs.j2
A env/galaxy/templates/nginx/galaxy.tools.j2
A env/galaxy/templates/nginx/galaxydomains.j2
A env/galaxy/templates/nginx/galaxyproject.j2
A env/galaxy/templates/nginx/images-proxy.j2
A env/galaxy/templates/nginx/images.j2
A env/galaxy/templates/nginx/intron.j2
A env/galaxy/templates/nginx/jenkins.j2
A env/galaxy/templates/nginx/lists.j2
A env/galaxy/templates/nginx/moin.j2
A env/galaxy/templates/nginx/new.j2
A env/galaxy/templates/nginx/orval.j2
A env/galaxy/templates/nginx/sample-data.j2
A env/galaxy/templates/nginx/screencast.j2
A env/galaxy/templates/nginx/snpeff-data.j2
A env/galaxy/templates/nginx/toolshed.tools.j2
A env/galaxy/templates/nginx/training.j2
A env/galaxy/templates/nginx/wheels.j2
A env/galaxy/templates/nginx/wiki.j2
A env/galaxy/templates/nginx/wiki_hub_rewrites.conf.j2
A env/galaxy/templates/supervisor/pypiserver.j2
R galaxyenv/files/apache/galaxy-installers.conf
R galaxyenv/files/jenkins/jenkins_server_user_ssh_config
R galaxyenv/files/jenkins/jenkins_slave_user_ssh_config
R galaxyenv/files/orval/rsyncd.xml
R galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem
R galaxyenv/files/ssl/wildcard_cert.pem
R galaxyenv/group_vars/all.yml
R galaxyenv/group_vars/baseenv.yml
R galaxyenv/group_vars/cvmfsstratum0servers.yml
R galaxyenv/group_vars/cvmfsstratum1servers.yml
R galaxyenv/group_vars/ec2hosts.yml
R galaxyenv/group_vars/jenkinsservers.yml
R galaxyenv/group_vars/jenkinsslaves.yml
R galaxyenv/group_vars/listservers.yml
R galaxyenv/group_vars/liteenv.yml
R galaxyenv/group_vars/mailservers.yml
R galaxyenv/group_vars/starforgebuilders.yml
R galaxyenv/host_vars/athena.galaxyproject.org.yml
R galaxyenv/host_vars/chouffe.galaxyproject.org.yml
R galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml
R galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml
R galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml
R galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml
R galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml
R galaxyenv/host_vars/delirium.galaxyproject.org.yml
R galaxyenv/host_vars/duvel.galaxyproject.org.yml
R galaxyenv/host_vars/jetstream-iu0.galaxyproject.org.yml
R galaxyenv/host_vars/jetstream-tacc0.galaxyproject.org.yml
R galaxyenv/host_vars/leeroy.galaxyproject.org.yml
R galaxyenv/host_vars/n4.galaxyproject.org.yml
R galaxyenv/host_vars/n6.galaxyproject.org.yml
R galaxyenv/host_vars/orval.galaxyproject.org.yml
R galaxyenv/host_vars/westvleteren.galaxyproject.org.yml
R galaxyenv/inventory
R galaxyenv/library/README
R galaxyenv/library/cron.py
R galaxyenv/playbook.yml
R galaxyenv/secret_group_vars/all.yml
R galaxyenv/secret_group_vars/dockersslservers.yml
R galaxyenv/secret_group_vars/dockerswarmmanagers.yml
R galaxyenv/secret_group_vars/jenkinsslaves.yml
R galaxyenv/secret_group_vars/sslwebservers.yml
R galaxyenv/secret_host_vars/athena.galaxyproject.org.yml
R galaxyenv/secret_host_vars/biostar.usegalaxy.org.yml
R galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml
R galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/default.yml
R galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml
R galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml
R galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml
R galaxyenv/secret_host_vars/orval.galaxyproject.org.yml
R galaxyenv/secret_host_vars/radegast.galaxyproject.org.yml
R galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml
R galaxyenv/templates/nginx/bioarchive.j2
R galaxyenv/templates/nginx/cloudlaunch.j2
R galaxyenv/templates/nginx/depot.j2
R galaxyenv/templates/nginx/docs.j2
R galaxyenv/templates/nginx/duvel.j2
R galaxyenv/templates/nginx/eggs.j2
R galaxyenv/templates/nginx/galaxy.tools.j2
R galaxyenv/templates/nginx/galaxydomains.j2
R galaxyenv/templates/nginx/galaxyproject.j2
R galaxyenv/templates/nginx/images-proxy.j2
R galaxyenv/templates/nginx/images.j2
R galaxyenv/templates/nginx/intron.j2
R galaxyenv/templates/nginx/jenkins.j2
R galaxyenv/templates/nginx/lists.j2
R galaxyenv/templates/nginx/moin.j2
R galaxyenv/templates/nginx/new.j2
R galaxyenv/templates/nginx/orval.j2
R galaxyenv/templates/nginx/sample-data.j2
R galaxyenv/templates/nginx/screencast.j2
R galaxyenv/templates/nginx/snpeff-data.j2
R galaxyenv/templates/nginx/toolshed.tools.j2
R galaxyenv/templates/nginx/training.j2
R galaxyenv/templates/nginx/wheels.j2
R galaxyenv/templates/nginx/wiki.j2
R galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2
R galaxyenv/templates/supervisor/pypiserver.j2
Log Message:
-----------
Relocate galaxyenv to env/galaxy
Commit: a42ef24ee9383f66633bcdbe21af20fea637b873
https://github.com/galaxyproject/infrastructure-playbook/commit/a42ef24ee93…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
A common_env
R common_env/files/ssl/docker/ca-key.pem
R common_env/files/ssl/docker/ca.pem
R common_env/files/ssl/docker/ca.srl
R common_env/files/ssl/docker/client.pem
R common_env/files/ssl/docker/client_privatekey.yml
R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem
R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey…
R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem
R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek…
R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p…
R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat…
R common_env/files/ssl/docker_test/ca-key.pem
R common_env/files/ssl/docker_test/ca.pem
R common_env/files/ssl/docker_test/ca.srl
R common_env/files/ssl/docker_test/client.pem
R common_env/files/ssl/docker_test/client_privatekey.yml
R common_env/files/ssl/docker_test/iu-gie-test/server.pem
R common_env/files/ssl/docker_test/iu-gie-test/server_privatekey.yml
R common_env/files/ssl/rabbitmq/ca-key.pem
R common_env/files/ssl/rabbitmq/ca.pem
R common_env/files/ssl/rabbitmq/ca.srl
R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem
R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml
R common_env/files/ssl/wildcard_cert.pem
R common_env/group_vars/baseenv/vars.yml
R common_env/group_vars/baseenv/vault.yml
R common_env/group_vars/sslservers/vars.yml
R common_env/group_vars/sslservers/vault.yml
R common_env/secret_group_vars/sslwebservers.yml
R env/common
A env/common/files/ssl/docker/ca-key.pem
A env/common/files/ssl/docker/ca.pem
A env/common/files/ssl/docker/ca.srl
A env/common/files/ssl/docker/client.pem
A env/common/files/ssl/docker/client_privatekey.yml
A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem
A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey…
A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem
A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek…
A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p…
A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat…
A env/common/files/ssl/docker_test/ca-key.pem
A env/common/files/ssl/docker_test/ca.pem
A env/common/files/ssl/docker_test/ca.srl
A env/common/files/ssl/docker_test/client.pem
A env/common/files/ssl/docker_test/client_privatekey.yml
A env/common/files/ssl/docker_test/iu-gie-test/server.pem
A env/common/files/ssl/docker_test/iu-gie-test/server_privatekey.yml
A env/common/files/ssl/rabbitmq/ca-key.pem
A env/common/files/ssl/rabbitmq/ca.pem
A env/common/files/ssl/rabbitmq/ca.srl
A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem
A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml
A env/common/files/ssl/wildcard_cert.pem
A env/common/group_vars/sshservers/vars.yml
A env/common/group_vars/sshservers/vault.yml
A env/common/group_vars/sslservers/vars.yml
A env/common/group_vars/sslservers/vault.yml
A env/common/secret_group_vars/sslwebservers.yml
Log Message:
-----------
Reverse common_env <-> env/common symlink
Commit: a0ba5b2bd9a792c608339b4323daedecf921c0e1
https://github.com/galaxyproject/infrastructure-playbook/commit/a0ba5b2bd9a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M env/common/group_vars/sshservers/vars.yml
M env/common/group_vars/sshservers/vault.yml
A env/galaxy/group_vars/sshclients/vars.yml
A env/galaxy/group_vars/sshclients/vault.yml
A env/galaxy/group_vars/sshservers/common_vars.yml
A env/galaxy/group_vars/sshservers/common_vault.yml
A env/galaxy/group_vars/sshservers/vars.yml
A env/galaxy/group_vars/sshservers/vault.yml
M env/galaxy/inventory
R env/galaxy/secret_group_vars/all.yml
R jetstreamiuenv/group_vars/baseenv
A jetstreamiuenv/group_vars/sshservers/common_vars.yml
A jetstreamiuenv/group_vars/sshservers/common_vault.yml
A jetstreamiuenv/group_vars/sshservers/vars.yml
M jetstreamiuenv/inventory
R jetstreamtaccenv/group_vars/baseenv
A jetstreamtaccenv/group_vars/sshservers/common_vars.yml
A jetstreamtaccenv/group_vars/sshservers/common_vault.yml
A jetstreamtaccenv/group_vars/sshservers/vars.yml
M jetstreamtaccenv/inventory
R taccenv/group_vars/baseenv
A taccenv/group_vars/sshservers/common_vars.yml
A taccenv/group_vars/sshservers/common_vault.yml
A taccenv/group_vars/sshservers/vars.yml
M taccenv/inventory
Log Message:
-----------
Convert ssh keys out of the baseenv group to a separate sshkeys group,
allow hash merging by renaming to common_sshkeys
Commit: 99fe08fd5b10ce15eed7d70cec11263b11cf6c06
https://github.com/galaxyproject/infrastructure-playbook/commit/99fe08fd5b1…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
M common_roles
Log Message:
-----------
Update common_roles for users role improvements
Commit: 7dcb2ac12002fec9ea230fbec1c40b836e822e2a
https://github.com/galaxyproject/infrastructure-playbook/commit/7dcb2ac1200…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-26 (Thu, 26 Oct 2017)
Changed paths:
A env/galaxy/group_vars/dockersslservers/vars.yml
A env/galaxy/group_vars/dockersslservers/vault.yml
A env/galaxy/group_vars/dockerswarmmanagers/vars.yml
A env/galaxy/group_vars/dockerswarmmanagers/vault.yml
R env/galaxy/group_vars/jenkinsslaves.yml
A env/galaxy/group_vars/jenkinsslaves/vars.yml
A env/galaxy/group_vars/jenkinsslaves/vault.yml
R env/galaxy/secret_group_vars/dockersslservers.yml
R env/galaxy/secret_group_vars/dockerswarmmanagers.yml
R env/galaxy/secret_group_vars/jenkinsslaves.yml
Log Message:
-----------
Mostly convert the galaxy env to standard vars/vault group_vars
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fe919ae973…