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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 15 Dec '16

15 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 790e60af60093dcb8e26f093c3a87903605da206 https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 95daf69b372fa829325be561dc0a9907da0bea81 https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 4c07734f57453581666fd3994c44d583f3e319b9 https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.10' into release_16.01 Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 22fda449f9d4ff2ed21fe4e39080456120aaf95e https://github.com/galaxyproject/galaxy/commit/22fda449f9d4ff2ed21fe4e39080… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 42cda969281c2d3e2918eb0d376415154e22d1db https://github.com/galaxyproject/galaxy/commit/42cda969281c2d3e2918eb0d3764… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 74923463cf4139ef084b155467975c7040ba5561 https://github.com/galaxyproject/galaxy/commit/74923463cf4139ef084b15546797… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.10' into dev Commit: 5c01c01791ad79bef23388b6892de974ad7b6323 https://github.com/galaxyproject/galaxy/commit/5c01c01791ad79bef23388b6892d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Add security disclosure to release notes Commit: ad738447e7003429dfe43198a339a8bf78231287 https://github.com/galaxyproject/galaxy/commit/ad738447e7003429dfe43198a339… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge branch 'release_16.10' into dev Commit: c1397908cd1fc81b294849008b1e5ec1b1381660 https://github.com/galaxyproject/galaxy/commit/c1397908cd1fc81b294849008b1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10 Commit: 36895d1dce26efc5db8f172b5b329b5dcbc54202 https://github.com/galaxyproject/galaxy/commit/36895d1dce26efc5db8f172b5b32… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/498dddb03fe3...36895d1dce26

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 15 Dec '16

15 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 790e60af60093dcb8e26f093c3a87903605da206 https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 95daf69b372fa829325be561dc0a9907da0bea81 https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 4c07734f57453581666fd3994c44d583f3e319b9 https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_15.10' into release_16.01 Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 22fda449f9d4ff2ed21fe4e39080456120aaf95e https://github.com/galaxyproject/galaxy/commit/22fda449f9d4ff2ed21fe4e39080… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 42cda969281c2d3e2918eb0d376415154e22d1db https://github.com/galaxyproject/galaxy/commit/42cda969281c2d3e2918eb0d3764… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: 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: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 5c01c01791ad79bef23388b6892de974ad7b6323 https://github.com/galaxyproject/galaxy/commit/5c01c01791ad79bef23388b6892d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Add security disclosure to release notes Commit: c1397908cd1fc81b294849008b1e5ec1b1381660 https://github.com/galaxyproject/galaxy/commit/c1397908cd1fc81b294849008b1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10 Compare: https://github.com/galaxyproject/galaxy/compare/d2ab7e701c87...c1397908cd1f

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[galaxyproject/galaxy] ac581a: Improved documentation and design of integration t...
by GitHub 15 Dec '16

15 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac581a5453e6f43a4900d55d67a3c1bd75081f47 https://github.com/galaxyproject/galaxy/commit/ac581a5453e6f43a4900d55d67a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M run_tests.sh M test/base/api.py M test/base/integration_util.py M test/integration/test_resolvers.py Log Message: ----------- Improved documentation and design of integration tests. - Allow running through ``run_tests.sh``. - Enable more verbose test errors for Conda tests. - Refactor how integration tests depend on API testing (use a Mixin instead of subclassing conceptually conflicting TestCase classes). Commit: 00c6ee17b7f742efdd895fae44771edacba77c4b https://github.com/galaxyproject/galaxy/commit/00c6ee17b7f742efdd895fae4477… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh Log Message: ----------- Fix Jenkins script test for integration tests. Commit: b78287f1508db2c06f0c309ed8d3747adb4d17fa https://github.com/galaxyproject/galaxy/commit/b78287f1508db2c06f0c309ed8d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/base/driver_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/integration/retry_jobs_job_conf.xml A test/integration/retry_jobs_job_resource_parameters_conf.xml A test/integration/retry_runner.py A test/integration/test_retry_jobs.py M test/unit/jobs/test_mapper.py Log Message: ----------- Integration test for advanced job runner stuff. Set of test cases that cover job resource handlers and resubmit job destinations. Commit: 0559cff6e94b250ddd98275b119ab51b36491e34 https://github.com/galaxyproject/galaxy/commit/0559cff6e94b250ddd98275b119a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.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 R test/integration/retry_jobs_job_conf.xml R test/integration/retry_jobs_job_resource_parameters_conf.xml R test/integration/retry_runner.py A test/integration/test_job_resubmission.py R test/integration/test_retry_jobs.py Log Message: ----------- Implement resubmit on unknown failures. Commit: 7d52b28ab2ab0314cd4fa31108a6750cb9750ef3 https://github.com/galaxyproject/galaxy/commit/7d52b28ab2ab0314cd4fa31108a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/integration/resubmission_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Allow expressions in job_conf resubmission conditions. Since we allow dynamic job runners clearly job_conf.xml must be considered a trusted document. Still I know that some are uneasy with eval generally so I only allow a very safe subset of Python expressions in this job_conf document. Commit: 949d1224892861bd27207dd0799e2b356576c2cb https://github.com/galaxyproject/galaxy/commit/949d1224892861bd27207dd0799e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Fix preservation of resubmits for resubmitted jobs. Create an abstraction for the explicit handling of resubmits that is done during job recovery at startup. xref https://github.com/galaxyproject/galaxy/commit/5539a083e21b601bfd2f87fa3417… Commit: 7e338d790964f594ae67b33e6a72e1777e774b8c https://github.com/galaxyproject/galaxy/commit/7e338d790964f594ae67b33e6a72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add attempt to resubmission expression language. Commit: 325b0354754815d32ed458d212d8c1c192630b0b https://github.com/galaxyproject/galaxy/commit/325b0354754815d32ed458d212d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M test/integration/resubmission_job_conf.xml Log Message: ----------- Add a self re-submission test. Commit: 18eb1c8d0e4c3f7616d44fd177c90943695b7053 https://github.com/galaxyproject/galaxy/commit/18eb1c8d0e4c3f7616d44fd177c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_job_resource_parameters_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add seconds_running and seconds_since_queued to condition expression langauge. Commit: 334dfe1b116775466ef772a9d7a98d6247959ed0 https://github.com/galaxyproject/galaxy/commit/334dfe1b116775466ef772a9d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Allow (and test) using expressions in job re-submission delays. So you can backoff re-submission with ``delay="attempt * 30"`` for instance - which will cause a re-submission delay to increase by 30 seconds for each resubmission of a job. Commit: 521a585a23459714e9723903363ffa495918cc60 https://github.com/galaxyproject/galaxy/commit/521a585a23459714e9723903363f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M test/integration/resubmission_runners.py Log Message: ----------- Two lint fixes for #3291. Commit: 498dddb03fe33df71ec887a9c53311ce53069e31 https://github.com/galaxyproject/galaxy/commit/498dddb03fe33df71ec887a9c533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.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/model/__init__.py M run_tests.sh 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/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/unit/jobs/test_mapper.py Log Message: ----------- Merge pull request #3291 from jmchilton/integration_tests_0 Ready Integration Testing for Prime Time Compare: https://github.com/galaxyproject/galaxy/compare/ed4e87ecad31...498dddb03fe3

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[galaxyproject/galaxy] db63b1: Fix styling, we don't need to force rounded edges ...
by GitHub 15 Dec '16

15 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: db63b131c1728493a87901764c102dbc47f74f3f https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Fix styling, we don't need to force rounded edges here. Commit: ca24098883fda1c35241d4c380f8b0765de7bb95 https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/style/less/dataset.less M static/style/blue/base.css Log Message: ----------- Remove unused style, we can rely on the :last pseudoclasses for this. Commit: f8974acba2884dc2fc1728aaa81021708ad05493 https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa810… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Fix styling when only one visualization type exists Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes. Commit: 29cf7187233bbd031f07df4584f1bef55de612e4 https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Minor styling tweaks -- todo: swap from inline to class-based. Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7 https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.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/style/blue/base.css Log Message: ----------- Standard styles inclusion in .less, more styling to match rounded edges and spacing. Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8 https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M 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scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M 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scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/galaxy/workflow/editor.mako A test-data/bam_from_sam.bam A 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test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3 https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Don't rely on complex, absolute selector, use local element.find() Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / Commit: d2ab7e701c87f4292b655893103c7842900a47b5 https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.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 Log Message: ----------- build the client Commit: ed4e87ecad31f48ecefa11b7c9a7aae4c71939aa https://github.com/galaxyproject/galaxy/commit/ed4e87ecad31f48ecefa11b7c9a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/style/blue/base.css Compare: https://github.com/galaxyproject/galaxy/compare/da784093b368...ed4e87ecad31

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[galaxyproject/galaxy] db63b1: Fix styling, we don't need to force rounded edges ...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: db63b131c1728493a87901764c102dbc47f74f3f https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Fix styling, we don't need to force rounded edges here. Commit: ca24098883fda1c35241d4c380f8b0765de7bb95 https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/style/less/dataset.less M static/style/blue/base.css Log Message: ----------- Remove unused style, we can rely on the :last pseudoclasses for this. Commit: f8974acba2884dc2fc1728aaa81021708ad05493 https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa810… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Fix styling when only one visualization type exists Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes. Commit: 29cf7187233bbd031f07df4584f1bef55de612e4 https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Minor styling tweaks -- todo: swap from inline to class-based. Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7 https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.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/style/blue/base.css Log Message: ----------- Standard styles inclusion in .less, more styling to match rounded edges and spacing. Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8 https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M 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M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M 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scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/galaxy/workflow/editor.mako A test-data/bam_from_sam.bam A 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test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3 https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- Don't rely on complex, absolute selector, use local element.find() Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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 Log Message: ----------- The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / Commit: d2ab7e701c87f4292b655893103c7842900a47b5 https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.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 Log Message: ----------- build the client Compare: https://github.com/galaxyproject/galaxy/compare/329108f81021...d2ab7e701c87

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[galaxyproject/galaxy] bb8a5a: [16.10] Revert commands.shell changes from galaxyp...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6 https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f466… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42 https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. Commit: da784093b3683b3586075aed3c70e38c3adc7c22 https://github.com/galaxyproject/galaxy/commit/da784093b3683b3586075aed3c70… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4069da74292...da784093b368

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[galaxyproject/galaxy] bb4e7c: Add change_password functionality back to the user...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb4e7c1a64df3b3c7c5c5c6391310883726a0af4 https://github.com/galaxyproject/galaxy/commit/bb4e7c1a64df3b3c7c5c5c639131… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add change_password functionality back to the user controller. This was removed a bit too soon in https://github.com/galaxyproject/galaxy/commit/14e635aaee2699cb395443d802de…, without a replacement available. There's significant work involved in a replacement, so @guerler and I agreed to simply add the endpoint back for now. Commit: c4069da7429242bdbf7fb02da9716e4e8413512c https://github.com/galaxyproject/galaxy/commit/c4069da7429242bdbf7fb02da971… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3313 from dannon/password_reset_fixes Add change_password functionality back to the user controller. Compare: https://github.com/galaxyproject/galaxy/compare/e627f55be69a...c4069da74292

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[galaxyproject/galaxy] bb8a5a: [16.10] Revert commands.shell changes from galaxyp...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6 https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f466… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42 https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. Compare: https://github.com/galaxyproject/galaxy/compare/2c833499b130...329108f81021

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[galaxyproject/galaxy] b31c3b: Fix logo image when serving Galaxy from a subdirec...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b31c3b24ac82a52d095a6e808c3e489dc308c045 https://github.com/galaxyproject/galaxy/commit/b31c3b24ac82a52d095a6e808c3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix logo image when serving Galaxy from a subdirectory. Commit: e627f55be69aead2c8aec7dfe7f230c125cf2f7d https://github.com/galaxyproject/galaxy/commit/e627f55be69aead2c8aec7dfe7f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #3283 from jmchilton/logo_source Fix logo image when serving Galaxy from a subdirectory. Compare: https://github.com/galaxyproject/galaxy/compare/cf7119c474e2...e627f55be69a

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[galaxyproject/galaxy] 81a0cb: Update datatype converter tools
by GitHub 13 Dec '16

13 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81a0cbf4721d7279e3a5b901e1646380d797635b https://github.com/galaxyproject/galaxy/commit/81a0cbf4721d7279e3a5b901e164… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: 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_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 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/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/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 Log Message: ----------- Update datatype converter tools - dos2unix - Fix indentation - Add missing tool version - Remove deprecated <page> elements - Remove deprecated 'interpreter' attribute of <command> - Quote some data parameters in <command> - Remove some duplicated requirement Commit: ac8450f013284bc5b8502cfec0d64e809390ce02 https://github.com/galaxyproject/galaxy/commit/ac8450f013284bc5b8502cfec0d6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_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 M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml Log Message: ----------- Add CDATA. Use && to concatenate commands. Quote $chromInfo Commit: cf7119c474e294eae79320fa5a51e5cdb5fa5835 https://github.com/galaxyproject/galaxy/commit/cf7119c474e294eae79320fa5a51… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: 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 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 Log Message: ----------- Merge pull request #3305 from nsoranzo/converter_tools Update datatype converter tools Compare: https://github.com/galaxyproject/galaxy/compare/ad8d48c0a39d...cf7119c474e2

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