galaxy-commits June 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 8b2ae4: Copy PJAs when importing a workflow.
by GitHub 20 Jun '16

20 Jun '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 8b2ae464678e96c917ed06a82f158f7c3b97b34a https://github.com/galaxyproject/galaxy/commit/8b2ae464678e96c917ed06a82f15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-20 (Mon, 20 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Copy PJAs when importing a workflow. Commit: 5aaa1ecdf0cb9a015bbfaf68d02cdab30bf02335 https://github.com/galaxyproject/galaxy/commit/5aaa1ecdf0cb9a015bbfaf68d02c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-20 (Mon, 20 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #2518 from dannon/backport_to_1601_pjafix [16.01] Copy PJAs when importing a workflow. Compare: https://github.com/galaxyproject/galaxy/compare/75cdec9b4baa...5aaa1ecdf0cb

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[galaxyproject/galaxy] c7ffff: Copy PJAs when importing a workflow.
by GitHub 20 Jun '16

20 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7ffffbda76bd122098e777015f1a07eb5dcd339 https://github.com/galaxyproject/galaxy/commit/c7ffffbda76bd122098e777015f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-16 (Thu, 16 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Copy PJAs when importing a workflow. Commit: a902420b92aea83c7800d255cd62c7a299f7e4f4 https://github.com/galaxyproject/galaxy/commit/a902420b92aea83c7800d255cd62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-20 (Mon, 20 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #2508 from dannon/workflow_import_pja_fix Copy PJAs when importing a workflow. Compare: https://github.com/galaxyproject/galaxy/compare/1f82d009253f...a902420b92ae

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[galaxyproject/galaxy] 11cdc4: display TIFF in upload
by GitHub 20 Jun '16

20 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11cdc4703a7881b08bc5a55c9c3511c98dfbb0eb https://github.com/galaxyproject/galaxy/commit/11cdc4703a7881b08bc5a55c9c35… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-20 (Mon, 20 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- display TIFF in upload Commit: 1f82d009253f35eb34f39c6d716d3e13eaae0cd0 https://github.com/galaxyproject/galaxy/commit/1f82d009253f35eb34f39c6d716d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-20 (Mon, 20 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2516 from bgruening/display_tiff_in_upload display TIFF in upload Compare: https://github.com/galaxyproject/galaxy/compare/ac5907fa9f4a...1f82d009253f

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[galaxyproject/ansible-galaxy] 144b3c: Ensure tool_dependency_dir exists
by GitHub 17 Jun '16

17 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 144b3c6c7aac3d5c4af12f0910c720d1df519840 https://github.com/galaxyproject/ansible-galaxy/commit/144b3c6c7aac3d5c4af1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M defaults/main.yml M tasks/mutable_setup.yml Log Message: ----------- Ensure tool_dependency_dir exists Commit: 7ccdf33d5fe1123ead92a2228ca74a5a9e56598b https://github.com/galaxyproject/ansible-galaxy/commit/7ccdf33d5fe1123ead92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-17 (Fri, 17 Jun 2016) Changed paths: M defaults/main.yml M tasks/mutable_setup.yml Log Message: ----------- Merge pull request #14 from mvdbeek/create_tool_dependency_dir Ensure tool_dependency_dir exists Compare: https://github.com/galaxyproject/ansible-galaxy/compare/0f78dde618c3...7ccd…

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[galaxyproject/galaxy] 618c64: Fix two errors in sff_extract.py detected by flake...
by GitHub 16 Jun '16

16 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 618c644d2b1225d354192e8c18d4b4f62de0b532 https://github.com/galaxyproject/galaxy/commit/618c644d2b1225d354192e8c18d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-16 (Thu, 16 Jun 2016) Changed paths: M tools/filters/sff_extract.py Log Message: ----------- Fix two errors in sff_extract.py detected by flake8 -- either of these code paths would have thrown an exception and failed prior to this. Commit: ac5907fa9f4adbd92be1650333ee54279ffe63cb https://github.com/galaxyproject/galaxy/commit/ac5907fa9f4adbd92be1650333ee… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-16 (Thu, 16 Jun 2016) Changed paths: M tools/filters/sff_extract.py Log Message: ----------- Merge pull request #2509 from dannon/sff_extract_fixes Fix two errors in sff_extract.py detected by flake8 Compare: https://github.com/galaxyproject/galaxy/compare/9d84c0b883c6...ac5907fa9f4a

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[galaxyproject/galaxy] c8af30: UI, history: backport of 3672eda
by GitHub 16 Jun '16

16 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c8af30009b3201037e55ff26a7d26f1734ae1dc3 https://github.com/galaxyproject/galaxy/commit/c8af30009b3201037e55ff26a7d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-16 (Thu, 16 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- UI, history: backport of 3672eda (update using xhr date header) Commit: 70b40979968f1ec3c36f025e5639b879ad017ca1 https://github.com/galaxyproject/galaxy/commit/70b40979968f1ec3c36f025e5639… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-16 (Thu, 16 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- Merge pull request #2506 from carlfeberhard/twice-a-day [16.04] UI, history: backport of 3672eda Compare: https://github.com/galaxyproject/galaxy/compare/f3f0c30106a8...70b40979968f

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[galaxyproject/infrastructure-playbook] 7a5aca: Update influxdb to 0.13.0 config format, disable a...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7a5acabd2aff6cc7dea098697d80de384038e8a5 https://github.com/galaxyproject/infrastructure-playbook/commit/7a5acabd2af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Update influxdb to 0.13.0 config format, disable a few features.

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[galaxyproject/infrastructure-playbook] 5238ba: orval access changes
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5238ba593214adf3131a88b96e1e6276ccc404bd https://github.com/galaxyproject/infrastructure-playbook/commit/5238ba59321… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- orval access changes

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[galaxyproject/galaxy] f7a6a2: This is an extra hammer swing at #1531 / #1542, wh...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7a6a2323d188b2eca7ed03d26c59dbcb636b30b https://github.com/galaxyproject/galaxy/commit/f7a6a2323d188b2eca7ed03d26c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- This is an extra hammer swing at #1531 / #1542, which @rmarenco encountered. He said this resolves it. Commit: 5707954491e90682d5f04f3e631a3e6c8d4fdeb1 https://github.com/galaxyproject/galaxy/commit/5707954491e90682d5f04f3e631a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Try to refresh input_datasets.dataset before accessing creating_job -- this is yet another attempt to resolve this being unavailable at job finish time. Commit: 9d84c0b883c62a5913dfb9e56b895bceedf1690a https://github.com/galaxyproject/galaxy/commit/9d84c0b883c62a5913dfb9e56b89… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #2505 from dannon/bigger_hammer_remi_pja This is an extra hammer swing at #1531 / #1542 Compare: https://github.com/galaxyproject/galaxy/compare/4ef24d6ab8d1...9d84c0b883c6

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[galaxyproject/infrastructure-playbook] 678b59: Lower influxdb memory usage (hopefully)
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 678b5913992893dc10db0ef136c0dae07f2418f2 https://github.com/galaxyproject/infrastructure-playbook/commit/678b5913992… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Lower influxdb memory usage (hopefully)

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galaxy-commits June 2016