galaxy-commits May 2017

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 6a9491: add dev requirement
by GitHub 04 May '17

04 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a949120832c414a4b891b33bc7b7bda86802e83 https://github.com/galaxyproject/galaxy/commit/6a949120832c414a4b891b33bc7b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M scripts/bootstrap_history.py Log Message: ----------- add dev requirement remove nitesh and carl from devteam Commit: 5077b7ce0e55646242d741311487ca8c0f0cdeb9 https://github.com/galaxyproject/galaxy/commit/5077b7ce0e55646242d741311487… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #4008 from martenson/release-process-fix add dev requirement Compare: https://github.com/galaxyproject/galaxy/compare/d226390c1857...5077b7ce0e55

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[galaxyproject/galaxy] f78b57: Simplify RC creation in Makefile.
by GitHub 03 May '17

03 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f78b5709a55693313568c5bea5a08db3f083779b https://github.com/galaxyproject/galaxy/commit/f78b5709a55693313568c5bea5a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M Makefile Log Message: ----------- Simplify RC creation in Makefile. These commands fail without any harm and then prevent the important echo statements from printing that follow them. Commit: d226390c185799d03ce9e42cc2939ad2a1ae4e6a https://github.com/galaxyproject/galaxy/commit/d226390c185799d03ce9e42cc293… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M Makefile Log Message: ----------- Merge pull request #4011 from jmchilton/simplify_makefile_create_rc Simplify RC creation in Makefile. Compare: https://github.com/galaxyproject/galaxy/compare/8bc0100165f4...d226390c1857

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[galaxyproject/galaxy] 460d17: typo
by GitHub 03 May '17

03 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 460d1737beb5d6e3e966c33998a7d5d046ac3e87 https://github.com/galaxyproject/galaxy/commit/460d1737beb5d6e3e966c33998a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- typo Commit: 6ef7b9977a3ed936c02b3e7fadfd105bbaea9595 https://github.com/galaxyproject/galaxy/commit/6ef7b9977a3ed936c02b3e7fadfd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #4015 from erasche/remote-user-bug [17.05] Typo in remote user / user preferences exception Compare: https://github.com/galaxyproject/galaxy/compare/99317c77557e...6ef7b9977a3e

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[galaxyproject/galaxy] 8dd5b1: Pass hdca and element_identifier to _serve_raw
by GitHub 03 May '17

03 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 8dd5b153ed728591d3e44acb4271afc0210981f2 https://github.com/galaxyproject/galaxy/commit/8dd5b153ed728591d3e44acb4271… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Pass hdca and element_identifier to _serve_raw This is necessary for getting the new filenames introduced in #3985 if downloading tabular datatypes. Closes #4016. Commit: 99317c77557ed4daec4c36619ec90a45a51e35eb https://github.com/galaxyproject/galaxy/commit/99317c77557ed4daec4c36619ec9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4017 from mvdbeek/fix_new_download_names_tabular Pass hdca and element_identifier to _serve_raw Compare: https://github.com/galaxyproject/galaxy/compare/ce8f0dec0532...99317c77557e

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[galaxyproject/infrastructure-playbook] c030d1: Update Jupyter image
by GitHub 03 May '17

03 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c030d1b91b13dec07fa74d11f5c74645a14fa5da https://github.com/galaxyproject/infrastructure-playbook/commit/c030d1b91b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml Log Message: ----------- Update Jupyter image Commit: 1a034df83b5073b0aff779299dcec610cb3a0854 https://github.com/galaxyproject/infrastructure-playbook/commit/1a034df83b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M roles/stats/defaults/main.yml M roles/stats/tasks/main.yml A roles/stats/templates/galaxy_slurp.py.j2 M taccenv/group_vars/statsservers.yml M taccenv/secret_group_vars/stats.yml Log Message: ----------- Slurp stats from Galaxy DB for Grafana Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/7002b8f547…

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[galaxyproject/usegalaxy-playbook] ccd062: Add grafana for Main
by GitHub 03 May '17

03 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccd062f81075a8399f2b0a1be627dc69bf2d0be6 https://github.com/galaxyproject/usegalaxy-playbook/commit/ccd062f81075a839… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml M production/group_vars/galaxydbservers.yml M production/secret_vars/galaxydbservers.yml Log Message: ----------- Add grafana for Main

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[galaxyproject/usegalaxy-playbook] 49e404: Add grafana
by GitHub 03 May '17

03 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49e404c4f6d83c9870f6c666fd9eaeb698920c59 https://github.com/galaxyproject/usegalaxy-playbook/commit/49e404c4f6d83c98… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Add grafana

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[galaxyproject/galaxy] 8db51d: Update version to 17.05.rc1
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 8db51db70258463df762e6ed70f621f56d1a8d74 https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.rc1 Commit: ce8f0dec0532266bff5d277f8acc50a4c6a9b2b5 https://github.com/galaxyproject/galaxy/commit/ce8f0dec0532266bff5d277f8acc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4009 from jmchilton/version-17.05 [17.05] Update version to 17.05.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/aeed375c0286...ce8f0dec0532

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[galaxyproject/galaxy] 8db51d: Update version to 17.05.rc1
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8db51db70258463df762e6ed70f621f56d1a8d74 https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.rc1 Commit: cc97e9f379ac8233bffdcf089468fc1e96f4942e https://github.com/galaxyproject/galaxy/commit/cc97e9f379ac8233bffdcf089468… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.09.dev Commit: 5079b925e37822f5b62003d03a1f29f4ae36e1ab https://github.com/galaxyproject/galaxy/commit/5079b925e37822f5b62003d03a1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Log Message: ----------- Merge branch 'version-17.05' into version-17.09.dev Commit: 8bc0100165f4f39e76402303cf7d8fea73a6b200 https://github.com/galaxyproject/galaxy/commit/8bc0100165f4f39e76402303cf7d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4010 from jmchilton/version-17.09.dev Version 17.09.dev Compare: https://github.com/galaxyproject/galaxy/compare/06d0e4fce57f...8bc0100165f4

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[galaxyproject/galaxy] 609842: [17.05] Pin dependencies for linting Galaxy.
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 609842e558da5f60eef94809204b48204fc8158a https://github.com/galaxyproject/galaxy/commit/609842e558da5f60eef94809204b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- [17.05] Pin dependencies for linting Galaxy. Commit: aeed375c0286315c2b893d7b807d3522c5c21a36 https://github.com/galaxyproject/galaxy/commit/aeed375c0286315c2b893d7b807d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4012 from jmchilton/17.05_pin_release_linting [17.05] Pin dependencies for linting Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/06d0e4fce57f...aeed375c0286

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galaxy-commits May 2017