Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: a9280649b201dc8c1ce6e1601c5baaae211acbd7
https://github.com/galaxyproject/galaxy/commit/a9280649b201dc8c1ce6e1601c5b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message:
-----------
Sync job_script module with Pulsar to fix doctest.
Following test fails without this change and is fixed by it.
```
nosetests --with-doctest lib/galaxy/jobs/runners/util/job_script
```
I'm not sure why Travis doesn't pick this up - I should figure that out.
Commit: adbc66873a13dc3c6cbcbf86181f935d09fed490
https://github.com/galaxyproject/galaxy/commit/adbc66873a13dc3c6cbcbf86181f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message:
-----------
Merge pull request #2203 from jmchilton/doctest_fix
[16.04] Sync job_script module with Pulsar to fix doctest.
Compare: https://github.com/galaxyproject/galaxy/compare/e5290e1964fc...adbc66873a13
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1aa8eb980aac5503a6cf585241fe974899922557
https://github.com/galaxyproject/galaxy/commit/1aa8eb980aac5503a6cf585241fe…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-04 (Mon, 04 Apr 2016)
Changed paths:
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Attempted fix for server error on repo preview.
This should handle cases where the database record specifies a repository dependency, but the repository in question (and its downloadable changeset) has been updated since the dependency was created.
Commit: ad929f231076706167cd88274bcf7c074e74fac4
https://github.com/galaxyproject/galaxy/commit/ad929f231076706167cd88274bcf…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-05 (Tue, 05 Apr 2016)
Changed paths:
A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
A test/shed_functional/test_data/0550_files/filtering_1.0.tgz
A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz
A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz
A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz
A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz
A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml
Log Message:
-----------
Add test for server error with updated repository.
Commit: 8c3f458bca948fc5efda027a4e09b8b5b8289276
https://github.com/galaxyproject/galaxy/commit/8c3f458bca948fc5efda027a4e09…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
Log Message:
-----------
Correct docs and names.
Commit: f4993b782679096f2576e749b146c76b45397314
https://github.com/galaxyproject/galaxy/commit/f4993b782679096f2576e749b146…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
Log Message:
-----------
Fix one more travis error.
Commit: 78e2eef2fcb4bcc51f26307ee351a3c5a679c300
https://github.com/galaxyproject/galaxy/commit/78e2eef2fcb4bcc51f26307ee351…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
Log Message:
-----------
Fix another travis error that escaped my notice.
Commit: d8b0add9c20bf6aee7c96d1c6106178cbf72cb3d
https://github.com/galaxyproject/galaxy/commit/d8b0add9c20bf6aee7c96d1c6106…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M .ci/py3_sources.txt
M .gitignore
M Makefile
R buildbot_setup.sh
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/style/less/base.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/tool_data_table_conf.xml.sample
M contrib/galaxy.debian-init
A contrib/galaxy_supervisor.conf
A display_applications/biom/biom_simple.xml
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/config.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/issue1818.tabular
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/model/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/version.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/modules.py
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/util/shed_util_common.py
M run_tests.sh
M run_tool_shed.sh
M scripts/bootstrap_history.py
M scripts/functional_tests.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
A scripts/tool_shed/api/import_capsule.py
A scripts/tool_shed/api/remove_repository_registry_entry.py
A scripts/tool_shed/api/reset_metadata_on_repositories.py
A scripts/tool_shed/api/tool_shed_repository_revision_update.py
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh
A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample
A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
A scripts/tool_shed/clean_up_tool_dependency_directory.py
A scripts/tool_shed/deprecate_repositories_without_metadata.py
A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form-workflow.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/layout/menu.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/style/blue/base.css
M templates/sharing_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/visualization/gie.mako
R templates/webapps/galaxy/workflow/export.mako
M templates/webapps/galaxy/workflow/list.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/tool_shed/repository/view_changeset.mako
M test/base/driver_util.py
A test/base/integration_util.py
M test/casperjs/casperjs_runner.py
A test/integration/__init__.py
A test/integration/embedded_pulsar_job_conf.xml
A test/integration/test_pulsar_embedded.py
M test/shed_functional/base/twilltestcase.py
M test/unit/jobs/test_command_factory.py
M test/unit/tools/test_conda_resolution.py
A tool-data/biom_simple_display.loc.sample
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_bugfixes
Commit: afa353b6fd00eb0ecf1d4bac9d64751537cae12a
https://github.com/galaxyproject/galaxy/commit/afa353b6fd00eb0ecf1d4bac9d64…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
Log Message:
-----------
Return current changeset if it is latest.
Commit: d35d6a707f3b265b10b859714deec793ecf31a53
https://github.com/galaxyproject/galaxy/commit/d35d6a707f3b265b10b859714dee…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Update documentation.
Commit: 4c126af1b0137fad228f0254dab45b6bec8fb9da
https://github.com/galaxyproject/galaxy/commit/4c126af1b0137fad228f0254dab4…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Ensure legacy behavior remains unaltered.
Per to the logic change in shed_util_common.get_next_downloadable_changeset_revision,
this commit modifies some conditionals to check whether it previously would have returned
None.
Commit: e1b167b312385df2a02fb5c7d4c4c464e3733bd7
https://github.com/galaxyproject/galaxy/commit/e1b167b312385df2a02fb5c7d4c4…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
Log Message:
-----------
Remove extra else statement.
Commit: 50757a13baf060601b681795403ba503a8897ede
https://github.com/galaxyproject/galaxy/commit/50757a13baf060601b681795403b…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Fix test 0550.
Commit: c79d057ca459586f4a01d50158d36530d0cbb163
https://github.com/galaxyproject/galaxy/commit/c79d057ca459586f4a01d50158d3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
A test/shed_functional/test_data/0550_files/filtering_1.0.tgz
A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz
A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz
A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz
A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz
A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml
Log Message:
-----------
Merge pull request #2079 from davebx/api_install_bugfixes
Attempted fix for server error on repo preview.
Compare: https://github.com/galaxyproject/galaxy/compare/9b5fdbf9a497...c79d057ca459