- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 42a461: Fix linting of 16.07 broken with security patches.
by GitHub 23 Dec '16

23 Dec '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy 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. Compare: https://github.com/galaxyproject/galaxy/compare/8b75305c49c3...b400a15c78fa

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[galaxyproject/galaxy] a7818e: Remove workflow testing stuff in test/functional a...
by GitHub 23 Dec '16

23 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7818e306598e5aa800123578cdad7936c88f34f https://github.com/galaxyproject/galaxy/commit/a7818e306598e5aa800123578cda… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Remove workflow testing stuff in test/functional and references. There are more fully developed approaches including Planemo and wft4galaxy (https://github.com/phnmnl/wft4galaxy) Commit: 58c1828c4c268aa80f1fe62888227d64d63b65d2 https://github.com/galaxyproject/galaxy/commit/58c1828c4c268aa80f1fe6288822… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Merge pull request #3342 from jmchilton/remove_workflow_testing Remove workflow testing stuff in test/functional and references. Compare: https://github.com/galaxyproject/galaxy/compare/8463c8a2024e...58c1828c4c26

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[galaxyproject/infrastructure-playbook] 02bc15: Add n6 as Jenkins slave
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 02bc15217958781958e7e4771e99047af53a508d https://github.com/galaxyproject/infrastructure-playbook/commit/02bc1521795… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: A galaxyenv/files/jenkins/jenkins_server_user_ssh_config A galaxyenv/files/jenkins/jenkins_slave_user_ssh_config M galaxyenv/group_vars/jenkinsservers.yml M galaxyenv/group_vars/jenkinsslaves.yml A galaxyenv/host_vars/n6.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_group_vars/jenkinsslaves.yml R galaxyenv/secret_host_vars/n4.galaxyproject.org.yml Log Message: ----------- Add n6 as Jenkins slave

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[galaxyproject/galaxy] 05cd16: Fix explicit Docker container resolution.
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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: 2783212c754ee9449688ce89893ada18afc0b8af https://github.com/galaxyproject/galaxy/commit/2783212c754ee9449688ce89893a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 8463c8a2024eef59d4faded15fd40f7850d7de7e https://github.com/galaxyproject/galaxy/commit/8463c8a2024eef59d4faded15fd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3358 from jmchilton/dev_merge Merge latest release 16.10 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/cac828ee8e91...8463c8a2024e

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[galaxyproject/galaxy] 83d9dd: Expose job metrics
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83d9ddd0b3e090829e70b95ac6bd26b63179e40f https://github.com/galaxyproject/galaxy/commit/83d9ddd0b3e090829e70b95ac6bd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Expose job metrics Commit: ae87eb94131e2a0da8ebae4ca6137ba111072852 https://github.com/galaxyproject/galaxy/commit/ae87eb94131e2a0da8ebae4ca613… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Address the review comments Commit: cac828ee8e91a8e0f4671042702e6898157bfd4e https://github.com/galaxyproject/galaxy/commit/cac828ee8e91a8e0f4671042702e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Merge pull request #3344 from erasche/expose-metrics Expose metrics to non-admins Compare: https://github.com/galaxyproject/galaxy/compare/c000e68baae4...cac828ee8e91

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[galaxyproject/galaxy] 38d316: Fix history list selector
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38d3163b2c7d0e9c4e428f4884cbed971a2f5bae https://github.com/galaxyproject/galaxy/commit/38d3163b2c7d0e9c4e428f4884cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: 10720fa4f9e26b3feec1a90468f4ecc726a99c05 https://github.com/galaxyproject/galaxy/commit/10720fa4f9e26b3feec1a90468f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fixup and test core.history.yaml tour. Commit: c000e68baae47dc7624465dacc3c6aa0217ece0a https://github.com/galaxyproject/galaxy/commit/c000e68baae47dc7624465dacc3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3185 from dannon/tour_history_fixes History Introduction tour fixes for structural changes Compare: https://github.com/galaxyproject/galaxy/compare/7ae30948be60...c000e68baae4

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[galaxyproject/galaxy] 318e5a: Update UCSC_SERVERS list to include new SOE prefix...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 318e5a23ad0ef2d50debfe72a0366ec5fd8513c3 https://github.com/galaxyproject/galaxy/commit/318e5a23ad0ef2d50debfe72a036… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Update UCSC_SERVERS list to include new SOE prefix. Commit: 7ae30948be60e34bc7b54cbf74f23da45414bad1 https://github.com/galaxyproject/galaxy/commit/7ae30948be60e34bc7b54cbf74f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3345 from dannon/ucsc_redirect_fix Update UCSC_SERVERS list to include new(ish?) soe subdomain Compare: https://github.com/galaxyproject/galaxy/compare/306c64d1bc3c...7ae30948be60

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[galaxyproject/galaxy] 05cd16: Fix explicit Docker container resolution.
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/14549d0f1b20...17a752d1f2fb

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/5eafa8bae312...14549d0f1b20

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/22fda449f9d4...8b75305c49c3

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[galaxyproject/galaxy] 99000f: update rename dataset action to accept . in repeat...
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99000fbed3b6c13274a3ddf9eb58310cb40653f7 https://github.com/galaxyproject/galaxy/commit/99000fbed3b6c13274a3ddf9eb58… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'. e.g. for filter bam 0.0.1: #{input_bams_0.input_bam} and #{input_bams_0.input_bam|basename} work. And for filter bam 0.0.2: #{input_bams1} and #{input_bams2|basename} work. Commit: 306c64d1bc3cec871f38b522ad3f7bf8e0ca3a66 https://github.com/galaxyproject/galaxy/commit/306c64d1bc3cec871f38b522ad3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3197 from scholtalbers/workflows-rename-output-minor-update update rename dataset action to accept . in repeat input parameters Compare: https://github.com/galaxyproject/galaxy/compare/538447be76da...306c64d1bc3c

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[galaxyproject/galaxy] 96678f: More IPython to Jupyter changes
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96678f57ccef01f322a6c6525defaa73333e56d0 https://github.com/galaxyproject/galaxy/commit/96678f57ccef01f322a6c6525def… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- More IPython to Jupyter changes Follow-up on #3294. Commit: 538447be76da011508eb4a8784eefe2b9e45b270 https://github.com/galaxyproject/galaxy/commit/538447be76da011508eb4a8784ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #3333 from nsoranzo/followup_on_3294 More IPython to Jupyter changes Compare: https://github.com/galaxyproject/galaxy/compare/af90b42a68d1...538447be76da

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[galaxyproject/galaxy] c61be9: Prettier Job information page
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61be93b70fd65b4bccf5f8416b58086ae98a085 https://github.com/galaxyproject/galaxy/commit/c61be93b70fd65b4bccf5f8416b5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Prettier Job information page Commit: fe2ec33d0bb67b0cbf0ef9297b737592f4f938bb https://github.com/galaxyproject/galaxy/commit/fe2ec33d0bb67b0cbf0ef9297b73… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove empty header from non-admin view Commit: dd062b5ca8de36a43b133a58b09d374ce07d63bd https://github.com/galaxyproject/galaxy/commit/dd062b5ca8de36a43b133a58b09d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako Log Message: ----------- Remove replace, just don't add in first place Commit: 1c7055fe3b974d06c8e166e39ac1a53d2f078642 https://github.com/galaxyproject/galaxy/commit/1c7055fe3b974d06c8e166e39ac1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Split metric table into sections Commit: 4756cab4cbcca729e3db66f33a8d031b796eb8d2 https://github.com/galaxyproject/galaxy/commit/4756cab4cbcca729e3db66f33a8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove visual noise Commit: 64b0d0326097f96c7637bd6355ca790c4ef8d4be https://github.com/galaxyproject/galaxy/commit/64b0d0326097f96c7637bd6355ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- cleanup css a bit Commit: cc32dcae4be031a95c393fd4efee459d398ae9c7 https://github.com/galaxyproject/galaxy/commit/cc32dcae4be031a95c393fd4efee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.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 Log Message: ----------- Initial tool form and dataset detail selenium testing. - Test parameters and tables appear on dataset details page after running a tool. - Test a simple tool execution with an integer field. - Test re-run a tool. - Test a tool with a data drop down. - Improved select2 abstractions. Commit: 097cf7f0fbcce7bc82539e17c12f7355deeaa558 https://github.com/galaxyproject/galaxy/commit/097cf7f0fbcce7bc82539e17c12f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Job metrics: Sort metrics on displayed title not key used for database. Commit: ef1fd488241a18952df146d30852054ab27a4a63 https://github.com/galaxyproject/galaxy/commit/ef1fd488241a18952df146d30852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Fix bad merge in cc32dcae4be031a95c393fd4efee459d398ae9c7. Spotted by @erasche. Commit: a5af4d155f6e4ab549c50e51703de49ee3052d16 https://github.com/galaxyproject/galaxy/commit/a5af4d155f6e4ab549c50e51703d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix Python 3 linting error for #3340. Commit: af90b42a68d119118d3fd2845738ef4835799af1 https://github.com/galaxyproject/galaxy/commit/af90b42a68d119118d3fd2845738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.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 Log Message: ----------- Merge pull request #3340 from erasche/nicer_info_page Prettier Job Information Page Compare: https://github.com/galaxyproject/galaxy/compare/e407b4b2c722...af90b42a68d1

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[galaxyproject/galaxy] 9bb570: Allow admins to see API keys under REMOTE_USER
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bb570f62f8e6f135f2776808a6a92e91ec8b7cb https://github.com/galaxyproject/galaxy/commit/9bb570f62f8e6f135f2776808a6a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Allow admins to see API keys under REMOTE_USER Commit: e407b4b2c7226fc00d5cf2c42126ab83409bca7a https://github.com/galaxyproject/galaxy/commit/e407b4b2c7226fc00d5cf2c42126… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3338 from erasche/admin_see_apikeys Allow admins to see API keys under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/e1b54f60f20e...e407b4b2c722

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[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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: e1b54f60f20e13353d9742fb15ec4cfd2c48fd2e https://github.com/galaxyproject/galaxy/commit/e1b54f60f20e13353d9742fb15ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-20 (Tue, 20 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/43075015dd7b...e1b54f60f20e

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[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/553ec588ed11...5eafa8bae312

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[galaxyproject/galaxy] c36fbe: genbank datatype
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c36fbebb443ae5b5263ba6cad6ad36113bb52f44 https://github.com/galaxyproject/galaxy/commit/c36fbebb443ae5b5263ba6cad6ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- genbank datatype Commit: 5e2249c1b4698db4880fb74e422a903585bc3054 https://github.com/galaxyproject/galaxy/commit/5e2249c1b4698db4880fb74e422a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Address review concerns Commit: 43075015dd7bd81bef0394259f0a60721f4163df https://github.com/galaxyproject/galaxy/commit/43075015dd7bd81bef0394259f0a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3339 from erasche/genbank Genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/415ddbb3bf8d...43075015dd7b

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[galaxyproject/infrastructure-playbook] c436aa: Run CVMFS client on cvmfs1-psu0 and serve datacach...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c436aa3d213fb7b4caa3ca0a891c03be6e3ef24f https://github.com/galaxyproject/infrastructure-playbook/commit/c436aa3d213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M common_roles M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml Log Message: ----------- Run CVMFS client on cvmfs1-psu0 and serve datacache rsync from there

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev 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: 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: 415ddbb3bf8d44acdcabc29478544420a45fc7e4 https://github.com/galaxyproject/galaxy/commit/415ddbb3bf8d44acdcabc2947854… 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/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f83a1bacf653...415ddbb3bf8d

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/release_16.10 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/c1397908cd1f...553ec588ed11

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[galaxyproject/galaxy] 48bc9b: add an option to specify the port, which is used t...
by GitHub 17 Dec '16

17 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48bc9ba31d43af09823b66726af86c7cfb0b8bba https://github.com/galaxyproject/galaxy/commit/48bc9ba31d43af09823b66726af8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add an option to specify the port, which is used to connect the UIs Commit: f83a1bacf6531a3efe404e93faca924d5a01bd3f https://github.com/galaxyproject/galaxy/commit/f83a1bacf6531a3efe404e93faca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3328 from bgruening/ie_port_overwrite IE enhancement Compare: https://github.com/galaxyproject/galaxy/compare/02501b938724...f83a1bacf653

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[galaxyproject/galaxy] a473c0: Provide a fallback to old IPython named config opt...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a473c0787a42618d26269e79732f6e997016c9d2 https://github.com/galaxyproject/galaxy/commit/a473c0787a42618d26269e79732f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Provide a fallback to old IPython named config option... ... as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/3294#pullrequestreview-12532937. Commit: 02501b938724ce7a788c6e6d91b7b506e0e5f25b https://github.com/galaxyproject/galaxy/commit/02501b938724ce7a788c6e6d91b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #3325 from jmchilton/juypter_fixes Provide a fallback to old IPython named config option... Compare: https://github.com/galaxyproject/galaxy/compare/a504e8ea7be4...02501b938724

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[galaxyproject/galaxy] 27673f: Addition of Genome fasta file loading in local IGV...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27673f5e08b67d432a0bd369aea6eac248ba8f93 https://github.com/galaxyproject/galaxy/commit/27673f5e08b67d432a0bd369aea6… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter Commit: 8cc2efb74f6679aee72cfdbc35a592d7abd2f4dc https://github.com/galaxyproject/galaxy/commit/8cc2efb74f6679aee72cfdbc35a5… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- removal of old commented line Commit: 1d0f15d1750e88dc1bf6ba835be2561771f99ce6 https://github.com/galaxyproject/galaxy/commit/1d0f15d1750e88dc1bf6ba835be2… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M display_applications/igv/genome_fasta.xml Log Message: ----------- Edit of Authors Commit: f4070ba9815ffacd28523f6e87398dea42271e8f https://github.com/galaxyproject/galaxy/commit/f4070ba9815ffacd28523f6e8739… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Syntax cleaning Commit: a504e8ea7be42940800dcb67d2c00d478868fb2c https://github.com/galaxyproject/galaxy/commit/a504e8ea7be42940800dcb67d2c0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Merge pull request #3327 from Delphine-L/IGV_display_fasta Addition of IGV display for genome fasta file Compare: https://github.com/galaxyproject/galaxy/compare/2845bfaf9609...a504e8ea7be4

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[galaxyproject/galaxy] 58a3a5: Fix linting of gff_filter_by_attribute.
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58a3a5b71b00c974b19eae514b09abfc04b74170 https://github.com/galaxyproject/galaxy/commit/58a3a5b71b00c974b19eae514b09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 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: 2845bfaf9609e55e785a71606ec535a225e7529d https://github.com/galaxyproject/galaxy/commit/2845bfaf9609e55e785a71606ec5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-16 (Fri, 16 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 #3324 from jmchilton/fix_lint_security Fix linting of gff_filter_by_attribute. Compare: https://github.com/galaxyproject/galaxy/compare/f4282c8672df...2845bfaf9609

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[galaxyproject/galaxy] 6fd77d: Preliminary fix for mapping tools with paired
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd77db920d088ba6ebc64a4ac8ab7524d5ce654 https://github.com/galaxyproject/galaxy/commit/6fd77db920d088ba6ebc64a4ac8a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Preliminary fix for mapping tools with paired collection input over list:paired collections. Commit: 1aba7549debca136048d2850dae28b1185e30469 https://github.com/galaxyproject/galaxy/commit/1aba7549debca136048d2850dae2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Add inherit_format tag to paired_collection_map_over_structured_like tool Commit: 55eac47d0fe9083c84afc613f451bfa68649b4d8 https://github.com/galaxyproject/galaxy/commit/55eac47d0fe9083c84afc613f451… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Fix test tool -- functional test framework appears to not support mapping over test-data Commit: a39941a3c57f0cf1d0db848debfed4d54c321627 https://github.com/galaxyproject/galaxy/commit/a39941a3c57f0cf1d0db848debfe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Add failing test for structured_like paired input Commit: cbd9f68f760178b113b624078372f955b486d32e https://github.com/galaxyproject/galaxy/commit/cbd9f68f760178b113b624078372… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Fixup test case for #3209. Commit: f4282c8672df5fb1f4d1f401c0209e1c6f253ca5 https://github.com/galaxyproject/galaxy/commit/f4282c8672df5fb1f4d1f401c020… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3209 from mvdbeek/fix_paired_list Fix for mapping tools with paired collection input and a structured_like tag over list:paired collections Compare: https://github.com/galaxyproject/galaxy/compare/147de088177c...f4282c8672df

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