- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 483e87: Fix dropdown zindex handling for history panels
by GitHub 08 May '18

08 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 483e879ca6fee1e58b6f9c99bf07291064ad5065 https://github.com/galaxyproject/galaxy/commit/483e879ca6fee1e58b6f9c99bf07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix dropdown zindex handling for history panels Commit: 7cc01380afd017c5cac2af2b2d735b2265774a68 https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Update bs4 style dropdowns, minor cleanup Commit: 7b558ddc5965f6223c862680341e81b345c73d82 https://github.com/galaxyproject/galaxy/commit/7b558ddc5965f6223c862680341e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6079 from dannon/dropdown-zindex-fix [18.05] Dropdown zindex fix Compare: https://github.com/galaxyproject/galaxy/compare/7d4109bac158...7b558ddc5965 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 880fa1: Add sandbox user to docker group on stratum0
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 880fa1080588dc830f10973dcaa0ab3a70de18ac https://github.com/galaxyproject/infrastructure-playbook/commit/880fa108058… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml Log Message: ----------- Add sandbox user to docker group on stratum0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] d3901e: Update text processing tools on Test
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d3901e9762ed456fdb3ab22ab89a7e5f434491a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3901e9762ed456f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update text processing tools on Test Commit: 6b5301798e5a50ccef030cbda0b5489f0ed8736b https://github.com/galaxyproject/usegalaxy-playbook/commit/6b5301798e5a50cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml Log Message: ----------- Run a branch of my repo on Test for testing job destination config params Commit: 21dbcefb57df0edd6af5a6c8e2e02018cb061fd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/21dbcefb57df0edd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test running tools w/ Singularity on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/55bc28e603e6...… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 9da558: Install singularity-runtime on roundup*
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9da558293a25e015543873545a43fdfc6f2fbe6e https://github.com/galaxyproject/infrastructure-playbook/commit/9da558293a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Install singularity-runtime on roundup* Commit: 5fcca9fece9b040426d4c9686eaddbc9ca5a10e7 https://github.com/galaxyproject/infrastructure-playbook/commit/5fcca9fece9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/common/files/ssl/docker/ca.srl A env/common/files/ssl/docker/client.pem A env/common/files/ssl/docker/client_privatekey.yml Log Message: ----------- Generate client cert for docker CA Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/cc99547bbe… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 2466bb: Increase UnkillableStepTimeout to try to stop node...
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2466bbc9bc2264b399afe51e4eb1fcd13b13dae5 https://github.com/galaxyproject/infrastructure-playbook/commit/2466bbc9bc2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase UnkillableStepTimeout to try to stop node drain Commit: cc99547bbeeb76c4c1616ad46e373946b1ac0001 https://github.com/galaxyproject/infrastructure-playbook/commit/cc99547bbee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: R env/galaxy/group_vars/cvmfsstratum1servers.yml A env/galaxy/group_vars/cvmfsstratum1servers/vars.yml A env/galaxy/group_vars/cvmfsstratum1servers/vault.yml M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vault.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/8e49e012ce… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 8e49e0: Add sandbox cvmfs repo for testing
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8e49e012ce57b3b15546c92f47e1cf63ca417abf https://github.com/galaxyproject/infrastructure-playbook/commit/8e49e012ce5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: R env/galaxy/group_vars/cvmfsstratum1servers.yml A env/galaxy/group_vars/cvmfsstratum1servers/vars.yml A env/galaxy/group_vars/cvmfsstratum1servers/vault.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Add sandbox cvmfs repo for testing **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 830561: Fix nested collection element downloads in UI.
by GitHub 07 May '18

07 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 830561a7bcd18a2aa80b8c0d5e1dc359ea9744ed https://github.com/galaxyproject/galaxy/commit/830561a7bcd18a2aa80b8c0d5e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Fix nested collection element downloads in UI. Fixes #6035. Commit: 7d4109bac1588cd67cc06b093b1fc18b509a69c9 https://github.com/galaxyproject/galaxy/commit/7d4109bac1588cd67cc06b093b1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge pull request #6073 from jmchilton/fix6035 [18.05] Fix nested collection element downloads in UI. Compare: https://github.com/galaxyproject/galaxy/compare/0cfac515b546...7d4109bac158 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 71c79f: File sizes were not being added
by GitHub 07 May '18

07 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71c79fda324877fb133f5f4194ac546be3041ee2 https://github.com/galaxyproject/galaxy/commit/71c79fda324877fb133f5f4194ac… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- File sizes were not being added Commit: 6a20984c57501b49a74dccb7992799a19abf7e6e https://github.com/galaxyproject/galaxy/commit/6a20984c57501b49a74dccb79927… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- try harder to handle unexpected values Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: f371d3f7094086ae183b3abc9cb3dc38ff361886 https://github.com/galaxyproject/galaxy/commit/f371d3f7094086ae183b3abc9cb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix paired identifier casting issue. Commit: 3b5d8ae99c5d6d8f040d6554320bb50e41fa58a4 https://github.com/galaxyproject/galaxy/commit/3b5d8ae99c5d6d8f040d6554320b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix x in column definition screen to eliminate correct def. Commit: 5bd2cbd80b35cc5ddddce808f17c13ce1381bc36 https://github.com/galaxyproject/galaxy/commit/5bd2cbd80b35cc5ddddce808f17c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Alter `extra_data` column on an oidc-related table from TXT to JSON. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Commit: 1b41cbba59bb09bdac305ff9de8d64dc4f873ee9 https://github.com/galaxyproject/galaxy/commit/1b41cbba59bb09bdac305ff9de8d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Merge pull request #6057 from VJalili/alter_extra_data [18.05] Alter the type of extra_data column of OIDC table. Commit: 96dcf54c438809c988eb063cf079bc7dbf4a5fe0 https://github.com/galaxyproject/galaxy/commit/96dcf54c438809c988eb063cf079… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix quota styling for new anchor/link. Commit: 6bb5fa02fc20fdfbb69085a5a0bfe57dfc7ef93a https://github.com/galaxyproject/galaxy/commit/6bb5fa02fc20fdfbb69085a5a0bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Use standard styling for quotameter; this fixes danger/warning/success indicators and visibility. Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: 89c12d6da2c797dbe2803768ad27657ac9a8e999 https://github.com/galaxyproject/galaxy/commit/89c12d6da2c797dbe2803768ad27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- More standard quota-meter-text color Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Commit: 011e76a72647a48a3415a36bd19c17e2688175df https://github.com/galaxyproject/galaxy/commit/011e76a72647a48a3415a36bd19c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6056 from jmchilton/rule_Builder_fixes_2 [18.05] Yet more rule builder fixes. Commit: b7c8fbe7c20c8c02cef182d7843a21d15346c1f1 https://github.com/galaxyproject/galaxy/commit/b7c8fbe7c20c8c02cef182d7843a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Tinker with brand-succcess, address the brightness concern (which makes many locations look better, at least to me) Commit: 19d06cb971c23444065df718260ac307293c8926 https://github.com/galaxyproject/galaxy/commit/19d06cb971c23444065df718260a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: d729c31ffd6e7198e5970eaeda2bcf3a65c20ba6 https://github.com/galaxyproject/galaxy/commit/d729c31ffd6e7198e5970eaeda2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 23b0169a17f3a4b1b705ee0dc0afe613e1cc29cd https://github.com/galaxyproject/galaxy/commit/23b0169a17f3a4b1b705ee0dc0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix non-capped usage display as well. Commit: 2a9e44e7a217f0ec3d48dd10811b23bd8da86c44 https://github.com/galaxyproject/galaxy/commit/2a9e44e7a217f0ec3d48dd10811b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #6065 from jmchilton/rule_fixes_4 [18.05] Rules - bug fix for apply_rules tool on nested collections. Commit: 7c44139dc82e6cf1486b23593c811e0f653af932 https://github.com/galaxyproject/galaxy/commit/7c44139dc82e6cf1486b23593c81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6062 from dannon/fix_quotameter_styling Fix quotameter styling Commit: ca48d49ea87b0716d27e8968c677b252c83b5ae9 https://github.com/galaxyproject/galaxy/commit/ca48d49ea87b0716d27e8968c677… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Style fix for published grid pages Commit: 8aaee18cae21f645170e14a32db0fc0f172cfd01 https://github.com/galaxyproject/galaxy/commit/8aaee18cae21f645170e14a32db0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Merge pull request #6067 from guerler/bootstrap_shared_grid Style fix for published grid pages Commit: 400bcf1b04adf6afb8e83efc6379e527c93fa810 https://github.com/galaxyproject/galaxy/commit/400bcf1b04adf6afb8e83efc6379… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-06 (Sun, 06 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #6064 from jmchilton/rule_fixes_3 [18.05] Rules - test case & bug fixes for adding cols from regex groups. Commit: 8255d1ccc819c88c7d5ee197bbb5ed9d49759fc4 https://github.com/galaxyproject/galaxy/commit/8255d1ccc819c88c7d5ee197bbb5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #5613 from erasche/fix-fraking-grt [18.01] File sizes not being annotated in GRT Commit: 0cfac515b546334e810caecf5cd02de8298de30a https://github.com/galaxyproject/galaxy/commit/0cfac515b546334e810caecf5cd0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: c67c4b4b82dd4280e9fcef4003a9956c6c0ca062 https://github.com/galaxyproject/galaxy/commit/c67c4b4b82dd4280e9fcef4003a9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M lib/galaxy/util/rules_dsl.py M scripts/grt/export.py M static/style/blue/base.css M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e49e31707fc...c67c4b4b82dd **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 71c79f: File sizes were not being added
by GitHub 07 May '18

07 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 71c79fda324877fb133f5f4194ac546be3041ee2 https://github.com/galaxyproject/galaxy/commit/71c79fda324877fb133f5f4194ac… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- File sizes were not being added Commit: 6a20984c57501b49a74dccb7992799a19abf7e6e https://github.com/galaxyproject/galaxy/commit/6a20984c57501b49a74dccb79927… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- try harder to handle unexpected values Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Commit: 8255d1ccc819c88c7d5ee197bbb5ed9d49759fc4 https://github.com/galaxyproject/galaxy/commit/8255d1ccc819c88c7d5ee197bbb5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #5613 from erasche/fix-fraking-grt [18.01] File sizes not being annotated in GRT Commit: 0cfac515b546334e810caecf5cd02de8298de30a https://github.com/galaxyproject/galaxy/commit/0cfac515b546334e810caecf5cd0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/400bcf1b04ad...0cfac515b546 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 71c79f: File sizes were not being added
by GitHub 07 May '18

07 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 71c79fda324877fb133f5f4194ac546be3041ee2 https://github.com/galaxyproject/galaxy/commit/71c79fda324877fb133f5f4194ac… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- File sizes were not being added Commit: 6a20984c57501b49a74dccb7992799a19abf7e6e https://github.com/galaxyproject/galaxy/commit/6a20984c57501b49a74dccb79927… Author: E Rasche <hxr(a)hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- try harder to handle unexpected values Commit: 8255d1ccc819c88c7d5ee197bbb5ed9d49759fc4 https://github.com/galaxyproject/galaxy/commit/8255d1ccc819c88c7d5ee197bbb5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #5613 from erasche/fix-fraking-grt [18.01] File sizes not being annotated in GRT Compare: https://github.com/galaxyproject/galaxy/compare/f7354c0eb3e2...8255d1ccc819 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 350c36: Add training subsection to depot
by GitHub 07 May '18

07 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 350c3636f6ec283a4290b05411512de5dd0a10c9 https://github.com/galaxyproject/infrastructure-playbook/commit/350c3636f6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vault.yml Log Message: ----------- Add training subsection to depot **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 19d06c: Rules - test case and bug fixes for adding cols fo...
by GitHub 07 May '18

07 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 19d06cb971c23444065df718260ac307293c8926 https://github.com/galaxyproject/galaxy/commit/19d06cb971c23444065df718260a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: 400bcf1b04adf6afb8e83efc6379e527c93fa810 https://github.com/galaxyproject/galaxy/commit/400bcf1b04adf6afb8e83efc6379… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-06 (Sun, 06 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #6064 from jmchilton/rule_fixes_3 [18.05] Rules - test case & bug fixes for adding cols from regex groups. Compare: https://github.com/galaxyproject/galaxy/compare/8aaee18cae21...400bcf1b04ad **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ca48d4: Style fix for published grid pages
by GitHub 05 May '18

05 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ca48d49ea87b0716d27e8968c677b252c83b5ae9 https://github.com/galaxyproject/galaxy/commit/ca48d49ea87b0716d27e8968c677… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Style fix for published grid pages Commit: 8aaee18cae21f645170e14a32db0fc0f172cfd01 https://github.com/galaxyproject/galaxy/commit/8aaee18cae21f645170e14a32db0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Merge pull request #6067 from guerler/bootstrap_shared_grid Style fix for published grid pages Compare: https://github.com/galaxyproject/galaxy/compare/7c44139dc82e...8aaee18cae21 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 96dcf5: Fix quota styling for new anchor/link.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 96dcf54c438809c988eb063cf079bc7dbf4a5fe0 https://github.com/galaxyproject/galaxy/commit/96dcf54c438809c988eb063cf079… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix quota styling for new anchor/link. Commit: 6bb5fa02fc20fdfbb69085a5a0bfe57dfc7ef93a https://github.com/galaxyproject/galaxy/commit/6bb5fa02fc20fdfbb69085a5a0bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Use standard styling for quotameter; this fixes danger/warning/success indicators and visibility. Commit: 89c12d6da2c797dbe2803768ad27657ac9a8e999 https://github.com/galaxyproject/galaxy/commit/89c12d6da2c797dbe2803768ad27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- More standard quota-meter-text color Commit: b7c8fbe7c20c8c02cef182d7843a21d15346c1f1 https://github.com/galaxyproject/galaxy/commit/b7c8fbe7c20c8c02cef182d7843a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Tinker with brand-succcess, address the brightness concern (which makes many locations look better, at least to me) Commit: 23b0169a17f3a4b1b705ee0dc0afe613e1cc29cd https://github.com/galaxyproject/galaxy/commit/23b0169a17f3a4b1b705ee0dc0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix non-capped usage display as well. Commit: 7c44139dc82e6cf1486b23593c811e0f653af932 https://github.com/galaxyproject/galaxy/commit/7c44139dc82e6cf1486b23593c81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6062 from dannon/fix_quotameter_styling Fix quotameter styling Compare: https://github.com/galaxyproject/galaxy/compare/2a9e44e7a217...7c44139dc82e **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d729c3: Rules - bug fix for apply_rules tool on nested col...
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: d729c31ffd6e7198e5970eaeda2bcf3a65c20ba6 https://github.com/galaxyproject/galaxy/commit/d729c31ffd6e7198e5970eaeda2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 2a9e44e7a217f0ec3d48dd10811b23bd8da86c44 https://github.com/galaxyproject/galaxy/commit/2a9e44e7a217f0ec3d48dd10811b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #6065 from jmchilton/rule_fixes_4 [18.05] Rules - bug fix for apply_rules tool on nested collections. Compare: https://github.com/galaxyproject/galaxy/compare/011e76a72647...2a9e44e7a217 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] f371d3: RuleBuilder - Fix paired identifier casting issue.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f371d3f7094086ae183b3abc9cb3dc38ff361886 https://github.com/galaxyproject/galaxy/commit/f371d3f7094086ae183b3abc9cb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix paired identifier casting issue. Commit: 3b5d8ae99c5d6d8f040d6554320bb50e41fa58a4 https://github.com/galaxyproject/galaxy/commit/3b5d8ae99c5d6d8f040d6554320b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix x in column definition screen to eliminate correct def. Commit: 011e76a72647a48a3415a36bd19c17e2688175df https://github.com/galaxyproject/galaxy/commit/011e76a72647a48a3415a36bd19c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6056 from jmchilton/rule_Builder_fixes_2 [18.05] Yet more rule builder fixes. Compare: https://github.com/galaxyproject/galaxy/compare/1b41cbba59bb...011e76a72647 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 8bee7b: Improve error message for mismatched data inputs
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Compare: https://github.com/galaxyproject/galaxy/compare/545b7a4fe2be...f7354c0eb3e2 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 5bd2cb: Alter `extra_data` column on an oidc-related table...
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 5bd2cbd80b35cc5ddddce808f17c13ce1381bc36 https://github.com/galaxyproject/galaxy/commit/5bd2cbd80b35cc5ddddce808f17c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Alter `extra_data` column on an oidc-related table from TXT to JSON. Commit: 1b41cbba59bb09bdac305ff9de8d64dc4f873ee9 https://github.com/galaxyproject/galaxy/commit/1b41cbba59bb09bdac305ff9de8d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Merge pull request #6057 from VJalili/alter_extra_data [18.05] Alter the type of extra_data column of OIDC table. Compare: https://github.com/galaxyproject/galaxy/compare/3292445872d9...1b41cbba59bb **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 624e90: [18.01] More tool state performance fixes.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Compare: https://github.com/galaxyproject/galaxy/compare/b35340c77f26...545b7a4fe2be **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 34cb08: disable influxdb max-row-limit
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 34cb08186081111e9672fff41ea29e727dc3c27c https://github.com/galaxyproject/infrastructure-playbook/commit/34cb0818608… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- disable influxdb max-row-limit to prevent data being cut off from display maybe we will need a limit eventually, but 10k seems too low Commit: 6ab46e62ce743debc531bd3aa4789e87bb0f2877 https://github.com/galaxyproject/infrastructure-playbook/commit/6ab46e62ce7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Merge pull request #23 from galaxyproject/martenson-patch-3 disable influxdb max-row-limit Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1daa68776b… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] dd3826: update Test
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd3826dc5bfd20e1c1fc094b84adbec6240c59f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/dd3826dc5bfd20e1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test Commit: 55bc28e603e61b5217f41316228e67ef03b2f74b https://github.com/galaxyproject/usegalaxy-playbook/commit/55bc28e603e61b52… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/7ceff21faf47...… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 34cb08: disable influxdb max-row-limit
by GitHub 03 May '18

03 May '18

Branch: refs/heads/martenson-patch-3 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 34cb08186081111e9672fff41ea29e727dc3c27c https://github.com/galaxyproject/infrastructure-playbook/commit/34cb0818608… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- disable influxdb max-row-limit to prevent data being cut off from display maybe we will need a limit eventually, but 10k seems too low **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 7ceff2: Uninstalled versions of snpeff and snpsift that we...
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7ceff21faf4737faa78265bac4f4561434dc42eb https://github.com/galaxyproject/usegalaxy-playbook/commit/7ceff21faf4737fa… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Uninstalled versions of snpeff and snpsift that were incorrectly loading in center pane **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 23762f: Docker fixes - release 18.05 edition.
by GitHub 03 May '18

03 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 23762f48a3385ffbf08112eb95739672a4656db7 https://github.com/galaxyproject/galaxy/commit/23762f48a3385ffbf08112eb9573… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Docker fixes - release 18.05 edition. - Rev to new container with 18.05 dependencies pre-installed. - Enable caching of Yarn stuffs to enable - Redo fix for git not working in node container - was mounting /etc/passwd but that wasn't compat. with Mac OS X, setting these environment variables are. - Rearrange startup script a bit to make it load faster (wait for Selenium right before the tests not before waiting for DB). - Fix random error in logs related to Selenium trying to read something in /root by passing -H to set the Selenium user's home directory. Commit: b84de1e82b36ae94be33ca4bf6e85e4c3ed748d2 https://github.com/galaxyproject/galaxy/commit/b84de1e82b36ae94be33ca4bf6e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Remove on-focus tooltips from rule builder. Commit: db8d7e65fedab9795cf41ef6b498358180c727dc https://github.com/galaxyproject/galaxy/commit/db8d7e65fedab9795cf41ef6b498… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix #6038. Commit: cb38b2495d9e42ee3e0e8acc13fc60214334c75f https://github.com/galaxyproject/galaxy/commit/cb38b2495d9e42ee3e0e8acc13fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6040 from jmchilton/remove_focus_tooltip [18.05] Two more rule builder fixes. Commit: b8e5893b0d4efee3d2b256bf08b95906a2fd370e https://github.com/galaxyproject/galaxy/commit/b8e5893b0d4efee3d2b256bf08b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix for building doubly nested collections. The late addition of validation code added for identifier uniqueness checking broke this I think. Commit: 618de018b9507a58945c318a4ac49447ff30023b https://github.com/galaxyproject/galaxy/commit/618de018b9507a58945c318a4ac4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #6029 from jmchilton/release_18.05_broken_tests [18.05] Docker fixes - release 18.05 edition. Commit: e11da5fba90d3ce4823481334888a602e229b588 https://github.com/galaxyproject/galaxy/commit/e11da5fba90d3ce4823481334888… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Fix jqplot: boxplot, histogram Fix heatmap clustering Fix nvd3 tool based types Remove global d3 object from heatmap and jqplot Commit: a8fe9a73942fd09a5e65ee51d7407952b362f6d4 https://github.com/galaxyproject/galaxy/commit/a8fe9a73942fd09a5e65ee51d740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- The link for specific individual history view has changed, but wasn't updated here in the error report. Commit: 6a2c678dcedf426319b77a24f686807ceff0b603 https://github.com/galaxyproject/galaxy/commit/6a2c678dcedf426319b77a24f686… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Bump bootstrap from 4.1.0 to 4.1.1 -- has a few bugfixes and hides the chatty and irrelevant (for us) deprecation warning on client build. Commit: ba6c3e6c625c8f2f024408541ad2196efdd5b1e4 https://github.com/galaxyproject/galaxy/commit/ba6c3e6c625c8f2f024408541ad2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Merge pull request #6047 from guerler/fix_charts [18.05] Fix and repack chart tool-based visualizations Commit: 666fec9f7b005676b1dd14e4a01a9a3df3861968 https://github.com/galaxyproject/galaxy/commit/666fec9f7b005676b1dd14e4a01a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Merge pull request #6052 from dannon/bs4_411 [18.05] Bump bootstrap from 4.1.0 to 4.1.1 Commit: 3829b0727d4ef05bdc1680f38babac7ac152350d https://github.com/galaxyproject/galaxy/commit/3829b0727d4ef05bdc1680f38bab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M templates/display_common.mako Log Message: ----------- Fix one more use of histories/view Commit: 8b733df8953431f16b2bd12e4cdd49090115e082 https://github.com/galaxyproject/galaxy/commit/8b733df8953431f16b2bd12e4cdd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/tools/errors.py M templates/display_common.mako Log Message: ----------- Merge pull request #6051 from dannon/fix_tool_error_report [18.05] Fix tool error report history view link Commit: 3292445872d9333753728828528947dc802a30be https://github.com/galaxyproject/galaxy/commit/3292445872d93337537288285289… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6045 from jmchilton/remove_focus_tooltip [18.05] Fix for building doubly nested collections. Commit: 3e49e31707fc0539b859fb11bbfd841fb38dda44 https://github.com/galaxyproject/galaxy/commit/3e49e31707fc0539b859fb11bbfd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/package.json M client/yarn.lock M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M lib/galaxy/tools/errors.py M run_tests.sh M static/style/blue/base.css M templates/display_common.mako M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/459384b060e1...3e49e31707fc **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b8e589: Fix for building doubly nested collections.
by GitHub 03 May '18

03 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b8e5893b0d4efee3d2b256bf08b95906a2fd370e https://github.com/galaxyproject/galaxy/commit/b8e5893b0d4efee3d2b256bf08b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix for building doubly nested collections. The late addition of validation code added for identifier uniqueness checking broke this I think. Commit: 3292445872d9333753728828528947dc802a30be https://github.com/galaxyproject/galaxy/commit/3292445872d93337537288285289… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6045 from jmchilton/remove_focus_tooltip [18.05] Fix for building doubly nested collections. Compare: https://github.com/galaxyproject/galaxy/compare/8b733df89534...3292445872d9 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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