- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 91c5b7: Fix upload to respect explicit name override on pa...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91c5b76667f28523bddde96171cd38af5f1ca2ba https://github.com/galaxyproject/galaxy/commit/91c5b76667f28523bddde96171cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-31 (Sat, 31 Dec 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: 9843e404b70b58616e55cf26e8a514a8df628771 https://github.com/galaxyproject/galaxy/commit/9843e404b70b58616e55cf26e8a5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3377 from jmchilton/upload_fix Fix upload to respect explicit name override on pasted uploads. Compare: https://github.com/galaxyproject/galaxy/compare/5a1caa5912a5...9843e404b70b

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[galaxyproject/galaxy] a78ae1: Fix tool shed pre-population against current dev.
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a78ae1bb7149199122f7dd2f8fd6b09599eb3ca4 https://github.com/galaxyproject/galaxy/commit/a78ae1bb7149199122f7dd2f8fd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix tool shed pre-population against current dev. I don't know how this ever worked to be honest - but these changes make a lot of sense. I think there was another bug somewhere that prevented this bug from exhibiting itself. Commit: b75ee68d9f6305646a55d816fb1173210e36eab9 https://github.com/galaxyproject/galaxy/commit/b75ee68d9f6305646a55d816fb11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Run Galaxy tests in --dockerize mode as UID of tester. Fixes #1541 and should really help Jenkins clean up after itself. Commit: 5a1caa5912a515b35257a2e8b911293c2eb7aad1 https://github.com/galaxyproject/galaxy/commit/5a1caa5912a515b35257a2e8b911… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3387 from jmchilton/docker_fix Docker Testing Fixes (for Jenkins for instance) Compare: https://github.com/galaxyproject/galaxy/compare/387c08b39b63...5a1caa5912a5

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[galaxyproject/galaxy] 8b7530: Merge pull request #3351 from jmchilton/galaxy_env...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: 387c08b39b63b9e3abf738b67267b04baf949a67 https://github.com/galaxyproject/galaxy/commit/387c08b39b63b9e3abf738b67267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9a876e659b3...387c08b39b63

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Commit: 05cd16f11cb523345894816ab6cc8165ebe71559 https://github.com/galaxyproject/galaxy/commit/05cd16f11cb523345894816ab6cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 4969c4a308fd5bfc8bc52739b024765147af49e8 https://github.com/galaxyproject/galaxy/commit/4969c4a308fd5bfc8bc52739b024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 14549d0f1b202a720dfc2dbb1f6501fc2cd8fd49 https://github.com/galaxyproject/galaxy/commit/14549d0f1b202a720dfc2dbb1f65… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. Commit: 17a752d1f2fbc19fdccbd9dd24ca1bdfd26aae5e https://github.com/galaxyproject/galaxy/commit/17a752d1f2fbc19fdccbd9dd24ca… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: 8b538f17feb17eba11b3025a2dfb3ba35414a78e https://github.com/galaxyproject/galaxy/commit/8b538f17feb17eba11b3025a2dfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/plugins/tours/core.history.yaml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_tools.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Compare: https://github.com/galaxyproject/galaxy/compare/378ed53a33ee...8b538f17feb1

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[galaxyproject/galaxy] 8b7530: Merge pull request #3351 from jmchilton/galaxy_env...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/4d84b3faa178...4d73dfc2e03d

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[galaxyproject/galaxy] c36871: Set metadata on HDAs from dynamically discovered c...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Compare: https://github.com/galaxyproject/galaxy/compare/b400a15c78fa...5b3debc51088

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[galaxyproject/infrastructure-playbook] 2a9ee5: Add curl package to Jenkins slaves.
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2a9ee5c40bc7218875f8312f3a6401d21259b1eb https://github.com/galaxyproject/infrastructure-playbook/commit/2a9ee5c40bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Add curl package to Jenkins slaves. Commit: a345eb16ccb8bbb01183bcaed37df1e97e6cd549 https://github.com/galaxyproject/infrastructure-playbook/commit/a345eb16ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Merge pull request #12 from jmchilton/add_curl_to_jenkins Add curl package to Jenkins slaves. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/02bc152179…

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[galaxyproject/galaxy] e0e2d6: added nrrd datatype
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0e2d6da7e3184282b64784ca2c0c424a2a28b03 https://github.com/galaxyproject/galaxy/commit/e0e2d6da7e3184282b64784ca2c0… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added nrrd datatype Commit: 325b06928552604ad90c0c2183a724c04eb5e9b9 https://github.com/galaxyproject/galaxy/commit/325b06928552604ad90c0c2183a7… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- fixed default extension of nrrd Commit: b28051a8867d1e0be50869eee3ab416d7f2819c3 https://github.com/galaxyproject/galaxy/commit/b28051a8867d1e0be50869eee3ab… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fixed typo Commit: eb544104787835c63282e1b1342818bf1be6228e https://github.com/galaxyproject/galaxy/commit/eb544104787835c63282e1b13428… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- lint fixes Commit: c9a876e659b30e69bd17586e9c9f213c9a81dc1b https://github.com/galaxyproject/galaxy/commit/c9a876e659b30e69bd17586e9c9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3385 from ThomasWollmann/image_datatypes added nrrd image datatype Compare: https://github.com/galaxyproject/galaxy/compare/1ef96f031b81...c9a876e659b3

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[galaxyproject/galaxy] c7c6c5: Fix typo
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7c6c565da4d1ab32db3ce14b91eeb057c49da3b https://github.com/galaxyproject/galaxy/commit/c7c6c565da4d1ab32db3ce14b91e… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Fix typo ouptup instead of output in assertion message Commit: 1ef96f031b81c7f35ce57c1a376875be75d766e3 https://github.com/galaxyproject/galaxy/commit/1ef96f031b81c7f35ce57c1a3768… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Merge pull request #3384 from pvanheus/patch-1 Fix typo Compare: https://github.com/galaxyproject/galaxy/compare/a870ac887cf4...1ef96f031b81

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[galaxyproject/galaxy] a870ac: added STL datatype (#2679)
by GitHub 05 Jan '17

05 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a870ac887cf43881906badecb2db7413b25cb96c https://github.com/galaxyproject/galaxy/commit/a870ac887cf43881906badecb2db… Author: ThomasWollmann <ThomasWollmann(a)users.noreply.github.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- added STL datatype (#2679) * added STL datatype * added image support to rstudio IE * added image support to jupyter IE * changed boolean to lower case * lint * lint * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * lint

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[galaxyproject/usegalaxy-playbook] 1e7c06: Updated slide rotation.
by GitHub 04 Jan '17

04 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e7c06ad0d5307336246bfccf862248cb19e0a02 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e7c06ad0d530733… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: A files/galaxy/common/static/welcome_img/GAMe2017RegisterNow.png A files/galaxy/common/static/welcome_img/ImmPortGalaxy.png A files/galaxy/common/static/welcome_img/PAG2017.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

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[galaxyproject/galaxy] 968b97: harmonised the use of capital and small letters
by GitHub 04 Jan '17

04 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 968b97a0ac81cd65397c6e2c0de538b2be16c6a7 https://github.com/galaxyproject/galaxy/commit/968b97a0ac81cd65397c6e2c0de5… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 7588e9df3d7b0d1cc3da0090aa062cea91dce8ea https://github.com/galaxyproject/galaxy/commit/7588e9df3d7b0d1cc3da0090aa06… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added image datatypes Commit: 88e838c587e4425f940dc19cd9848e8f12f42b35 https://github.com/galaxyproject/galaxy/commit/88e838c587e4425f940dc19cd984… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added tiff subtypes Commit: f4eadd71fd1da0a18863cd7e1718369cdf9af03d https://github.com/galaxyproject/galaxy/commit/f4eadd71fd1da0a18863cd7e1718… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 47e0d5d8103c22741555faab1063d1ad5b698e03 https://github.com/galaxyproject/galaxy/commit/47e0d5d8103c22741555faab1063… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added hamatsu sub datatypes Commit: f46d8ad739aed601f02c07b60c69c29f12c3b189 https://github.com/galaxyproject/galaxy/commit/f46d8ad739aed601f02c07b60c69… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 560813d908461cbeeeadf04c0fce487ac4ff9b35 https://github.com/galaxyproject/galaxy/commit/560813d908461cbeeeadf04c0fce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3380 from ThomasWollmann/image_datatypes Added image datatypes Compare: https://github.com/galaxyproject/galaxy/compare/7bac8bbc786b...560813d90846

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[galaxyproject/galaxy] 8d4f99: Limit adjusting Galaxy's Python environment to leg...
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d4f9955a66c94604634d436a4262cfef395b3e5 https://github.com/galaxyproject/galaxy/commit/8d4f9955a66c94604634d436a426… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Limit adjusting Galaxy's Python environment to legacy tools. Don't expose Galaxy's environment to tools unless there is evidence we need to. This should restrict future bugs by limitting what tools are exposed to Galaxy's internals and will fix bugs related to Conda dependencies masking Galaxy - such as #2994. Should fix #2994. Rebased with language and tool best practice fixes thanks to @mvdbeek. Commit: 7bac8bbc786ba9697cf1e0a0e8597c8d06aa1721 https://github.com/galaxyproject/galaxy/commit/7bac8bbc786ba9697cf1e0a0e859… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #3364 from jmchilton/clean_python Limit adjusting Galaxy's Python environment to legacy tools. Compare: https://github.com/galaxyproject/galaxy/compare/85333d4be474...7bac8bbc786b

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[galaxyproject/galaxy]
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/upgrade_conda Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] e350c8: Use a newer conda version by default
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e350c8b0517410e65f82e0c1276ef727ac6ae0ec https://github.com/galaxyproject/galaxy/commit/e350c8b0517410e65f82e0c1276e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Use a newer conda version by default Commit: 85333d4be47478d6e6107316a15776488f987e46 https://github.com/galaxyproject/galaxy/commit/85333d4be47478d6e6107316a157… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3378 from galaxyproject/upgrade_conda Use a newer conda version by default Compare: https://github.com/galaxyproject/galaxy/compare/29e5bd4915f8...85333d4be474

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[galaxyproject/galaxy]
by GitHub 03 Jan '17

03 Jan '17

Branch: refs/heads/conda_channel Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 487506: Fix automatic handling of Jenkins BUILD_NUMBER in ...
by GitHub 01 Jan '17

01 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 487506cc79d105f318f6a03e7a6f397ae765b9e8 https://github.com/galaxyproject/galaxy/commit/487506cc79d105f318f6a03e7a6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix automatic handling of Jenkins BUILD_NUMBER in Dockerized tests. Follow up #3368, this fix is also needed. I think we are getting closer... xref #3199 xref #3360 Commit: 29e5bd4915f8ff7128e1740723c4c9bb66c665d0 https://github.com/galaxyproject/galaxy/commit/29e5bd4915f8ff7128e1740723c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3370 from jmchilton/integration_tests_2 Fix automatic handling of Jenkins BUILD_NUMBER in Dockerized tests. Compare: https://github.com/galaxyproject/galaxy/compare/408254f93528...29e5bd4915f8

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[galaxyproject/galaxy] 74dfcd: cache deps on the fly when first used
by GitHub 01 Jan '17

01 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74dfcd32891b5a24b9c255097f780143cc28a104 https://github.com/galaxyproject/galaxy/commit/74dfcd32891b5a24b9c255097f78… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- cache deps on the fly when first used Commit: 9dbe766e42d3c22d09c5809823b8fec144ac5966 https://github.com/galaxyproject/galaxy/commit/9dbe766e42d3c22d09c5809823b8… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- add build_cache_on_first_run option Commit: 26ba67083ca8bbf33134a6caa032792a1d27f907 https://github.com/galaxyproject/galaxy/commit/26ba67083ca8bbf33134a6caa032… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- make travis happy Commit: 1a0dde830c3e9f33a02564d824fe0c468b5724cf https://github.com/galaxyproject/galaxy/commit/1a0dde830c3e9f33a02564d824fe… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- change option name and default value Commit: 408254f935288e8a1be007de3b633285e5ac61a7 https://github.com/galaxyproject/galaxy/commit/408254f935288e8a1be007de3b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3348 from abretaud/fill_cache Cache depencencies on the fly when first used Compare: https://github.com/galaxyproject/galaxy/compare/9654618a0afd...408254f93528

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[galaxyproject/galaxy] 52e4b6: Remove seemingly unused file sort_gtf.py.
by GitHub 01 Jan '17

01 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 52e4b6e89e862ce2a9e3897782a0836272be6581 https://github.com/galaxyproject/galaxy/commit/52e4b6e89e862ce2a9e3897782a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: R tools/filters/gff/sort_gtf.py Log Message: ----------- Remove seemingly unused file sort_gtf.py. Added in df28aec040f05f2d97856f5d8c4f07ba2a7e1966 - not used in that commit. Commit: 9654618a0afdaa1e5c6fd63a627800a6025a7bfa https://github.com/galaxyproject/galaxy/commit/9654618a0afdaa1e5c6fd63a6278… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: R tools/filters/gff/sort_gtf.py Log Message: ----------- Merge pull request #3362 from jmchilton/remove_sort Remove seemingly unused file sort_gtf.py. Compare: https://github.com/galaxyproject/galaxy/compare/bb80c842777e...9654618a0afd

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[galaxyproject/galaxy] e350c8: Use a newer conda version by default
by GitHub 01 Jan '17

01 Jan '17

Branch: refs/heads/upgrade_conda Home: https://github.com/galaxyproject/galaxy Commit: e350c8b0517410e65f82e0c1276ef727ac6ae0ec https://github.com/galaxyproject/galaxy/commit/e350c8b0517410e65f82e0c1276e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Use a newer conda version by default

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[galaxyproject/galaxy] 132e28: Bug fix for masthead webhook if Galaxy.page is und...
by GitHub 29 Dec '16

29 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 132e284d371992995c14eefbc299110533ec48b4 https://github.com/galaxyproject/galaxy/commit/132e284d371992995c14eefbc299… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: ef82eec6109721c4a5c2f4ab2e760f73bf46c7ce https://github.com/galaxyproject/galaxy/commit/ef82eec6109721c4a5c2f4ab2e76… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh M Makefile M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/dataset.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/webpack.config.js A display_applications/igv/genome_fasta.xml M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M doc/source/project/organization.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/install_manager.py M run_tests.sh M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_mapper.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merging with dev Commit: bb80c842777efd0ffd980060410cb72b253f9f45 https://github.com/galaxyproject/galaxy/commit/bb80c842777efd0ffd980060410c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3349 from bgruening/mastheadwebhookextend Masthead Webhook bug fix Compare: https://github.com/galaxyproject/galaxy/compare/4c22cefadd87...bb80c842777e

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[galaxyproject/galaxy] 3ec365: Fix auto creation of XUnit reports for Jenkins.
by GitHub 26 Dec '16

26 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ec3653adb4e796eb97625c339d03cba78ace726 https://github.com/galaxyproject/galaxy/commit/3ec3653adb4e796eb97625c339d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix auto creation of XUnit reports for Jenkins. This is why Jenkins isn't picking up reports for integration and Selenium tests automatically. Commit: 4c22cefadd877a4ea5a78a24cda56c62504dfe96 https://github.com/galaxyproject/galaxy/commit/4c22cefadd877a4ea5a78a24cda5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3368 from jmchilton/fix_jenkins_xunit_reports Fix auto creation of XUnit reports for Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/d4f70648898a...4c22cefadd87

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[galaxyproject/galaxy] 0383f5: Remove defunct script run_selenium_tests.sh.
by GitHub 26 Dec '16

26 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0383f5abc199fef22541adda9020fa84b8e98239 https://github.com/galaxyproject/galaxy/commit/0383f5abc199fef22541adda9020… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: R scripts/run_selenium_tests.sh Log Message: ----------- Remove defunct script run_selenium_tests.sh. Commit: d4f70648898a58b50613224cda82ea88f1b12934 https://github.com/galaxyproject/galaxy/commit/d4f70648898a58b50613224cda82… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: R scripts/run_selenium_tests.sh Log Message: ----------- Merge pull request #3367 from jmchilton/remove_script Remove defunct script run_selenium_tests.sh. Compare: https://github.com/galaxyproject/galaxy/compare/261524e57fd3...d4f70648898a

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[galaxyproject/galaxy] f34bb5: Don't override Global tempfile.tmpdir for tests.
by GitHub 26 Dec '16

26 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f34bb5e1f66e47ae13396f8ab8d8336aa635a255 https://github.com/galaxyproject/galaxy/commit/f34bb5e1f66e47ae13396f8ab8d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-24 (Sat, 24 Dec 2016) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py Log Message: ----------- Don't override Global tempfile.tmpdir for tests. Tests may bring up multiple Galaxy instances - for integration tests this leads to a longer temp path with each new Galaxy instance brought up. This in turn breaks Conda for tests on Jenkins. Commit: a0aa70baa0573ff891f51f3ffbc29e07dcf970a5 https://github.com/galaxyproject/galaxy/commit/a0aa70baa0573ff891f51f3ffbc2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-24 (Sat, 24 Dec 2016) Changed paths: M test/integration/test_job_resubmission.py Log Message: ----------- Fix broken integration test. It was simply checking the wrong condition. Commit: 261524e57fd353267016cfce3a7ca8de2b27d89c https://github.com/galaxyproject/galaxy/commit/261524e57fd353267016cfce3a7c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #3365 from jmchilton/integration_tests_1 Attempt to fix broken integration tests on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/58c1828c4c26...261524e57fd3

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[galaxyproject/galaxy] 3d155f: Fix history list selector
by GitHub 23 Dec '16

23 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 Compare: https://github.com/galaxyproject/galaxy/compare/17a752d1f2fb...4d84b3faa178

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