Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc12992... Author: guerler aysam.guerler@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/733a53adcfbd90bf3a02e2e1fadbc... Author: guerler aysam.guerler@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/3f07c7b52e1128ad3902ded6723eb... Author: guerler aysam.guerler@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/5c3a0e1df06a1690a132498398298... Author: guerler aysam.guerler@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/854b24bb009c46c8e48eb799aef3b... Author: John Chilton jmchilton@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/553ec588ed11effb3be665c92a3a7... Author: Dannon Baker dannon.baker@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/5eafa8bae312182a58f27e55bb93a... Author: Daniel Blankenberg dan.blankenberg@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/05cd16f11cb523345894816ab6cc8... Author: John Chilton jmchilton@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/fe2a1d8ade4fbda158ae035c78133... Author: John Chilton jmchilton@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/4969c4a308fd5bfc8bc52739b0247... Author: John Chilton jmchilton@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/8b75305c49c3e9fe3fb4665177af9... Author: Nicola Soranzo nsoranzo@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/14549d0f1b202a720dfc2dbb1f650... Author: Björn Grüning bjoern@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/17a752d1f2fbc19fdccbd9dd24ca1... Author: Björn Grüning bjoern@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/42a461353bc2dd07f60daf33a42e6... Author: John Chilton jmchilton@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/69fe5ae83ae53cb84a2d0bdd9ea53... Author: John Chilton jmchilton@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/3d155f0be0c91dbfe891394261c08... Author: Dannon Baker dannon.baker@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/b57a961f250968d6d62eff142b4ee... Author: John Chilton jmchilton@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/b400a15c78faba3b873ecf1ce2237... Author: Martin Cech cech.marten@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/4d84b3faa17872d1ebe22a1b8c622... Author: Martin Cech cech.marten@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/c3687114d6f2f14df49af9a3fee6d... Author: John Chilton jmchilton@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/5b3debc510888bd44ae55700fad8e... Author: Dannon Baker dannon.baker@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/4d73dfc2e03de4c7eaabfd2f6fadd... Author: Dannon Baker dannon.baker@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/8b538f17feb17eba11b3025a2dfb3... Author: Dannon Baker dannon.baker@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