Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 16dfca86e69597796e60e604ae410dcf6667291c https://github.com/galaxyproject/galaxy/commit/16dfca86e69597796e60e604ae410... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: 78c866fd34181ecda09488b6d19d2e37f6c69d02 https://github.com/galaxyproject/galaxy/commit/78c866fd34181ecda09488b6d19d2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation condition Commit: a44f30140990c93aa92b8cb5f0f87b819942b116 https://github.com/galaxyproject/galaxy/commit/a44f30140990c93aa92b8cb5f0f87... Author: guerler <aysam.guerler@gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M test/unit/tools/test_select_parameters.py Log Message: ----------- Revise contradicting test case, workflow injection through api attempts full validation without available datasets Commit: d9d51d362e8ef3197e01c0440289e60a50ad85e8 https://github.com/galaxyproject/galaxy/commit/d9d51d362e8ef3197e01c0440289e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add break to interrupt loop Commit: 2cf95d8a134bb84cec0408b016e751fc840327c1 https://github.com/galaxyproject/galaxy/commit/2cf95d8a134bb84cec0408b016e75... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M config/galaxy.ini.sample M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst A lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py 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/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/checkers.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/run.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/repository_types/metadata.py M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_HistoryManager.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: 7610f82a421edb422b8ba8f7731a1ae23fb9ac41 https://github.com/galaxyproject/galaxy/commit/7610f82a421edb422b8ba8f7731a1... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- fix markup for button links on sharing template (ff would fail to generate images) turn of autocomplete Commit: 574740d0b299d9cd84d9065f4746204f6399d891 https://github.com/galaxyproject/galaxy/commit/574740d0b299d9cd84d9065f47462... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Reset exception retries after successful job status check Commit: 08fb160b38fbcd9bcdfd776bb75ae5c92ca002d1 https://github.com/galaxyproject/galaxy/commit/08fb160b38fbcd9bcdfd776bb75ae... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2481 from martenson/fix-html-sharing [16.04] fix markup for button links on sharing template Commit: 4cf8d691e525142125af56b0627f804eb1bddd7c https://github.com/galaxyproject/galaxy/commit/4cf8d691e525142125af56b0627f8... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix image generation for workflows with missing tools currently this ends up with a server error Commit: fdf9520783ae55795a01e4092b1d6718c5fca5b4 https://github.com/galaxyproject/galaxy/commit/fdf9520783ae55795a01e4092b1d6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- drop unnecessary raise and fix capitalization incorporate comments of Bjoern and Nicola Commit: 43694be8647e3d1686b6c4fa80d0300bb9c96d42 https://github.com/galaxyproject/galaxy/commit/43694be8647e3d1686b6c4fa80d03... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge pull request #2456 from guerler/fix_building_mode [16.04] Relax validation condition for dynamic parameters Commit: 5245e8a693fc3633762f29a468b84e3487083133 https://github.com/galaxyproject/galaxy/commit/5245e8a693fc3633762f29a468b84... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2488 from martenson/wrap-svg-for-missing-tools [16.04] fix image generation for workflows with missing tools Commit: b3a32ac2e19afda605f26f989bf3e16eaa1d27af https://github.com/galaxyproject/galaxy/commit/b3a32ac2e19afda605f26f989bf3e... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/sharing.mako M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: 0017b3e9405e5e77904364025889c88cf0991744 https://github.com/galaxyproject/galaxy/commit/0017b3e9405e5e77904364025889c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add IUC channel to the list Commit: ec0d97327b0bf234021f5a3f5ab261b491baa091 https://github.com/galaxyproject/galaxy/commit/ec0d97327b0bf234021f5a3f5ab26... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2490 from bgruening/iuc_conda_channel [16.04] Add IUC conda channel Commit: 6ccfd13ab4e500774a40a54deba949d29f719f2c https://github.com/galaxyproject/galaxy/commit/6ccfd13ab4e500774a40a54deba94... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2487 from nsoranzo/release_16.04_reset_exception_retries [16.04] Reset exception retries after successful job status check Commit: 20f035dce887e5fcd04a5d7bdec92f80ba1fc9e2 https://github.com/galaxyproject/galaxy/commit/20f035dce887e5fcd04a5d7bdec92... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/sharing.mako M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'release_16.04' into dev Conflicts: test/unit/tools/test_select_parameters.py Compare: https://github.com/galaxyproject/galaxy/compare/c797d2bc9e99...20f035dce887