galaxy-commits January 2016

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[galaxyproject/galaxy] bf5bf7: Tour cleanup, remove a few globals.
by GitHub 30 Jan '16

30 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf5bf73e827337f3481fcbd8c6e1a34ffc0058ea https://github.com/galaxyproject/galaxy/commit/bf5bf73e827337f3481fcbd8c6e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Tour cleanup, remove a few globals. Commit: f8e6a55ab7a9048cdf1dbb87f7393e4535d43e03 https://github.com/galaxyproject/galaxy/commit/f8e6a55ab7a9048cdf1dbb87f739… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.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/onload.js Log Message: ----------- Swap to standard url parsing function from our js utils. Commit: 3deb005e99c609a9c5cee60b301027c4f6ec0df4 https://github.com/galaxyproject/galaxy/commit/3deb005e99c609a9c5cee60b3010… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #1621 from dannon/tour_cleanup Tour cleanup, remove a few globals. Compare: https://github.com/galaxyproject/galaxy/compare/76624949bc31...3deb005e99c6

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[galaxyproject/galaxy] 4ae49f: Fix module/step border style in workflow canvas
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4ae49fbfec952a2087a9cf3f9b9940f86fd05220 https://github.com/galaxyproject/galaxy/commit/4ae49fbfec952a2087a9cf3f9b99… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fix module/step border style in workflow canvas Commit: 44336b289bd5ba7d9911bf1c1fcc0a604fda7358 https://github.com/galaxyproject/galaxy/commit/44336b289bd5ba7d9911bf1c1fcc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1620 from guerler/fix_module_border_000 [16.01] Fix module/step border style in workflow canvas Compare: https://github.com/galaxyproject/galaxy/compare/81535c5778b7...44336b289bd5

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[galaxyproject/galaxy] 28c4b4: Various improvements to the heartbeat:
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28c4b49e8de240bde1fe4acefac32cbcc516afc4 https://github.com/galaxyproject/galaxy/commit/28c4b49e8de240bde1fe4acefac3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/util/heartbeat.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Various improvements to the heartbeat: - Dump on `SIGUSR1` - Configurable dump period (including "no periodic dump, signal only") - Default log filename now includes server_name so logs do not clobber eachother - Configurable/templateable log filename - Catch more sleeping threads - Use write() instead of print Commit: 148b4099bff3ed54f97a0c20c8b4f46e64969989 https://github.com/galaxyproject/galaxy/commit/148b4099bff3ed54f97a0c20c8b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Move heartbeat import to the global imports, do not attempt to register a None signal handler Commit: 76624949bc31555d7142b5e7476d3e60e5d08fa7 https://github.com/galaxyproject/galaxy/commit/76624949bc31555d7142b5e7476d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/util/heartbeat.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #1614 from natefoo/heartbeat-improvements Various improvements to the heartbeat Compare: https://github.com/galaxyproject/galaxy/compare/670a5f2c85fe...76624949bc31

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[galaxyproject/galaxy] cb09c3: Fix line wrapping for peek of tabular files.
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cb09c35a07e3b9f8ca7e4eb5e8d37ffacdee6253 https://github.com/galaxyproject/galaxy/commit/cb09c35a07e3b9f8ca7e4eb5e8d3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix line wrapping for peek of tabular files. Commit: 81535c5778b70001bfeb3da5690eba6426ea4638 https://github.com/galaxyproject/galaxy/commit/81535c5778b70001bfeb3da5690e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1500 from blankenberg/peek-fix [16.01] Fix line wrapping for peek of tabular files. Compare: https://github.com/galaxyproject/galaxy/compare/685fd1560e98...81535c5778b7

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[galaxyproject/usegalaxy-playbook] d8c80f: Update Test and Main
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d8c80fd42dd5a3e9c1cc8c5c7681689b0a7386d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/d8c80fd42dd5a3e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 390c1f: Always install a specific version of Galaxy pip in...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 390c1fc275ba7128f22f533b0b512b0bc517e521 https://github.com/galaxyproject/galaxy/commit/390c1fc275ba7128f22f533b0b51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always install a specific version of Galaxy pip in common_startup.sh. Commit: 46471d61e4349bba2d0c702de18f91a5b201bb66 https://github.com/galaxyproject/galaxy/commit/46471d61e4349bba2d0c702de18f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip < 1.6 cannot parse requirement specifiers to the `install` command that contain a `+` in the version. For these older versions, directly install the wheel or install from the sdist. Technically 1.4 and later can install wheels, but in testing, only 1.5+ was able to install them properly with their scripts. The new heredoc execute and redirect syntax is Bourne-compatible. pip --pre is no longer necessary since the Galaxy pip version is no longer a development version of pip. Commit: 60062b020dc2b753e5b8f034272e0b982b8c2f6f https://github.com/galaxyproject/galaxy/commit/60062b020dc2b753e5b8f034272e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip 1.6 -> 6.0, thanks @nsoranzo Commit: 685fd1560e98e6d885d6cf627b691d2228807974 https://github.com/galaxyproject/galaxy/commit/685fd1560e98e6d885d6cf627b69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1595 from natefoo/fix-pip-wheel-version [16.01] Always install a specific version of Galaxy pip in common_startup.sh. Compare: https://github.com/galaxyproject/galaxy/compare/27685377f629...685fd1560e98

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[galaxyproject/ansible-galaxy]
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/tags/0.6.2 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 3f8e11: Fix pip at 8.0.0
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3f8e1140b73629dd4cbf1c326533493e0bc80fb5 https://github.com/galaxyproject/ansible-galaxy/commit/3f8e1140b73629dd4cbf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-24 (Sun, 24 Jan 2016) Changed paths: M tasks/dependencies.yml Log Message: ----------- Fix pip at 8.0.0 Commit: 001cf5a411cea597229c7e9bae10aff86c4e7c55 https://github.com/galaxyproject/ansible-galaxy/commit/001cf5a411cea597229c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Make pip version confogurable. Commit: 9adce55fd265229089ae2709892ea7d2d8cff148 https://github.com/galaxyproject/ansible-galaxy/commit/9adce55fd265229089ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- pip at version 8.0.2, no --pre. Commit: 6209af56b96b4b326b63c8c6a8a8282f81094ce5 https://github.com/galaxyproject/ansible-galaxy/commit/6209af56b96b4b326b63… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Merge pull request #9 from ARTbio/fix_pip_version Fix pip at 8.0.0 Compare: https://github.com/galaxyproject/ansible-galaxy/compare/2f4cbc0969fc...6209…

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[galaxyproject/galaxy] 33ba1f: Link from the 16.01 announcement to the Admin whee...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33ba1face9e1f1bf025f37dc4e508143972845dc https://github.com/galaxyproject/galaxy/commit/33ba1face9e1f1bf025f37dc4e50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Link from the 16.01 announcement to the Admin wheels documentation, document the process of adding new wheels. Commit: 27685377f629c536e56189e795bc91bb8caf0736 https://github.com/galaxyproject/galaxy/commit/27685377f629c536e56189e795bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1612 from natefoo/admin-docs [16.01] Additional documentation regarding wheels Commit: 670a5f2c85fe153b79db1a37eb39f39ffa20b761 https://github.com/galaxyproject/galaxy/commit/670a5f2c85fe153b79db1a37eb39… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9264d90ea471...670a5f2c85fe

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[galaxyproject/galaxy] a077b0: Remove recovery hack for REALLY old jobs.
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a077b04809ff4ce44a534bbf61151a904accd6a0 https://github.com/galaxyproject/galaxy/commit/a077b04809ff4ce44a534bbf6115… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Remove recovery hack for REALLY old jobs. No more upgrading Galaxy straight from 2012 to 2016. Commit: 9264d90ea471214b09666b82781acd49d84f19ec https://github.com/galaxyproject/galaxy/commit/9264d90ea471214b09666b82781a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #1574 from jmchilton/remove_old_job_hack Remove recovery hack for REALLY old jobs. Compare: https://github.com/galaxyproject/galaxy/compare/db221325dac1...9264d90ea471

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galaxy-commits January 2016