galaxy-commits December 2016

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[galaxyproject/galaxy] 132e28: Bug fix for masthead webhook if Galaxy.page is und...
by GitHub 28 Dec '16

28 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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[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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galaxy-commits December 2016