- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b1f4a0: Fix initial conda version at 4.0.5
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1f4a0f61aeb8ddfec26c4b51bf92bdd50606c91 https://github.com/galaxyproject/galaxy/commit/b1f4a0f61aeb8ddfec26c4b51bf9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: ba6a0a36476cd5db46777e99b84b6440ec6073b0 https://github.com/galaxyproject/galaxy/commit/ba6a0a36476cd5db46777e99b84b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2869 from mvdbeek/upgrade_conda_instead_of_downgrading Fix initial conda version at 4.0.5 Compare: https://github.com/galaxyproject/galaxy/compare/0bd1ea108e7f...ba6a0a36476c

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[galaxyproject/galaxy] f6c1aa: Create a new trans method for getting the most rec...
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6c1aa0770508c552f074771078a4b7cc4cce400 https://github.com/galaxyproject/galaxy/commit/f6c1aa0770508c552f074771078a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Create a new trans method for getting the most recently touched history. Swap several uses of get_history (with create=True, only), to use this new functionality where it makes sense. Commit: 0bd1ea108e7f6000759583afd3e6d2d7daa3e7be https://github.com/galaxyproject/galaxy/commit/0bd1ea108e7f6000759583afd3e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2870 from dannon/histories.most_recent_v_default Create a new trans method for getting the most recently touched history. Compare: https://github.com/galaxyproject/galaxy/compare/e64503697302...0bd1ea108e7f

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[galaxyproject/galaxy] d86ee3: Add the <conda_prefix> in 12. and fix typo
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d86ee3706089e59868c16a3352ce61e0257dbb40 https://github.com/galaxyproject/galaxy/commit/d86ee3706089e59868c16a3352ce… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Add the <conda_prefix> in 12. and fix typo I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda). And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``). Commit: 579ea41085501139eebbbeb5b3f72c9c04c03e4c https://github.com/galaxyproject/galaxy/commit/579ea41085501139eebbbeb5b3f7… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update Marius advice Commit: e6450369730230bc844db67d3df05f1cffd3cdad https://github.com/galaxyproject/galaxy/commit/e6450369730230bc844db67d3df0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2871 from remimarenco/patch-8 Add the <conda_prefix> in 12. and fix typo Compare: https://github.com/galaxyproject/galaxy/compare/dbde38c951cd...e64503697302

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[galaxyproject/galaxy] 040dd3: Fix typo
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 040dd33980668ecb74a44dfc9c4e39e1a1339cef https://github.com/galaxyproject/galaxy/commit/040dd33980668ecb74a44dfc9c4e… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Fix typo Commit: dbde38c951cdbb539def102ca55ddf5a4da3ced2 https://github.com/galaxyproject/galaxy/commit/dbde38c951cdbb539def102ca55d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Merge pull request #2872 from remimarenco/patch-9 Fix typo Compare: https://github.com/galaxyproject/galaxy/compare/4ad0bee5523b...dbde38c951cd

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[galaxyproject/infrastructure-playbook] 308b9c: Only stratum 0s use the repo options
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 308b9c8862a75164b71d1465ef0b219e41997833 https://github.com/galaxyproject/infrastructure-playbook/commit/308b9c8862a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M roles/cvmfs/tasks/stratum0.yml Log Message: ----------- Only stratum 0s use the repo options Commit: dc0f1c9613afaa2a3b1096db53eedc7b62d83325 https://github.com/galaxyproject/infrastructure-playbook/commit/dc0f1c9613a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Node IPs were off by 1 Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6e5c654c9d…

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[galaxyproject/infrastructure-playbook] 6e5c65: Relaunched all Jetstream @ TACC resources
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6e5c654c9d4eaa9b0a2b50b8f5834650fd6ed7f2 https://github.com/galaxyproject/infrastructure-playbook/commit/6e5c654c9d4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml M jetstreamtaccenv/group_vars/all.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory M roles/cvmfs/tasks/stratum1.yml M roles/jetstream_nfs/tasks/server.yml Log Message: ----------- Relaunched all Jetstream @ TACC resources

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[galaxyproject/usegalaxy-playbook] 695d5f: Add gat2016 redirect
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 695d5f1841defb8424b145660401f30aef25864a https://github.com/galaxyproject/usegalaxy-playbook/commit/695d5f1841defb84… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Add gat2016 redirect

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[galaxyproject/usegalaxy-playbook] 86f45e: Update Test
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 86f45e53281aac412707fc132f735a33bdbc220e https://github.com/galaxyproject/usegalaxy-playbook/commit/86f45e53281aac41… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test Commit: 18d381fee4580da464383ae64e7d0442680352ad https://github.com/galaxyproject/usegalaxy-playbook/commit/18d381fee4580da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M templates/nginx/galaxy_main_installer.j2 M templates/nginx/galaxy_test.j2 Log Message: ----------- Installer moved to docker on galaxy04 Commit: 053e1eeaca7ac558661f303b073ab09e87851060 https://github.com/galaxyproject/usegalaxy-playbook/commit/053e1eeaca7ac558… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/98a878e0e3b6...…

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[galaxyproject/galaxy] 4f3c44: Move the registration of the start function into t...
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Move the registration of the start function into the ToolConfWatcher itself so it doesn't have to be called by things that instantiate it. Fixes #2831. Commit: 6631367b7cd4f2049426f3554eef6da626b83837 https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Unused import, cleanup for #2856 Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- fix inclusion of release notes in announcement Commit: c98331eddd3f8a57cedca313249798e1e45a9555 https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca3132497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix [16.07] Postfork tool conf watcher test fix Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d217… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix [16.07] Unused import cleanup for #2856 Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge pull request #2859 from martenson/fix-notes-include [16.07] fix inclusion of release notes in the announcement Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4 https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2863 from martenson/release_16.07 [16.07] backport disable conda_auto_init Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Commit: 4ad0bee5523b1a05423eaa21624ebe146412d423 https://github.com/galaxyproject/galaxy/commit/4ad0bee5523b1a05423eaa21624e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f9758f2871e3...4ad0bee5523b

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[galaxyproject/galaxy] 672414: Fix three conda bugs.
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Compare: https://github.com/galaxyproject/galaxy/compare/52768c0c4231...c01ce21e2cdb

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