galaxy-commits October 2016

galaxy-commits@lists.galaxyproject.org

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98 discussions

[galaxyproject/galaxy] 5e15d3: Use requests in driver_util for better proxy handl...
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e15d3b79d0fee4f469e2e3a1b0e2acdddeda15c https://github.com/galaxyproject/galaxy/commit/5e15d3b79d0fee4f469e2e3a1b0e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Use requests in driver_util for better proxy handling Commit: 9e299e93468041e984518d0992ad4b2041b681f6 https://github.com/galaxyproject/galaxy/commit/9e299e93468041e984518d0992ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #3013 from mvdbeek/proxy_planemo Use requests in driver_util for better proxy handling Compare: https://github.com/galaxyproject/galaxy/compare/2b10e2047293...9e299e934680

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[galaxyproject/galaxy] be3c34: Add rgb option for color picker
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be3c347a37fd0a84ff08fbac00af7816158db634 https://github.com/galaxyproject/galaxy/commit/be3c347a37fd0a84ff08fbac00af… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add rgb option for color picker Commit: f6d395c7cb9c217a2c653781a5702a1ae8449342 https://github.com/galaxyproject/galaxy/commit/f6d395c7cb9c217a2c653781a570… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix whitespace after comma Commit: 5f9bfd5fc078043bce9fa10c0063a1989887aae2 https://github.com/galaxyproject/galaxy/commit/5f9bfd5fc078043bce9fa10c0063… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add an XSD entry for this new feature. Commit: f599a7b8c025a60781216450f00a81c5a497bfd7 https://github.com/galaxyproject/galaxy/commit/f599a7b8c025a60781216450f00a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #15 from guerler/XSD_addition Add an XSD entry for this new feature. Commit: 2b10e2047293ee95ea8084657c55a5e354ce3b23 https://github.com/galaxyproject/galaxy/commit/2b10e2047293ee95ea8084657c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3006 from guerler/add_rgb_option Add rgb option for color picker Compare: https://github.com/galaxyproject/galaxy/compare/d0b9e2ca9f19...2b10e2047293

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[galaxyproject/galaxy] c6fca3: Remove unused value map argument from basic parame...
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6fca34428bdf62d74ff476f5a1bd4b2b9f97790 https://github.com/galaxyproject/galaxy/commit/c6fca34428bdf62d74ff476f5a1b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused value map argument from basic parameter handling Commit: f283a6248cc6638c58074286f7dfa3e34a2e1a00 https://github.com/galaxyproject/galaxy/commit/f283a6248cc6638c58074286f7df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add space Commit: e93c9b42d648537fed89569373d83f20ebeaf3c7 https://github.com/galaxyproject/galaxy/commit/e93c9b42d648537fed89569373d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove two unused private functions for data tool parameters Commit: a6da9ab00006fc21ebbf511f1210a9685ce9ddfa https://github.com/galaxyproject/galaxy/commit/a6da9ab00006fc21ebbf511f1210… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Rename private function to indicate public use Commit: d0b9e2ca9f19453a74a478426c3e2d2236bf8788 https://github.com/galaxyproject/galaxy/commit/d0b9e2ca9f19453a74a478426c3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #3007 from guerler/remove_unused_value_map Remove unused value map argument from basic parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/51aa341fe5ac...d0b9e2ca9f19

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[galaxyproject/usegalaxy-playbook] 20a067: Updated slide rotation on landing page.
by GitHub 06 Oct '16

06 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 20a0676a81a8504ac54e80a67110fbbffc190a31 https://github.com/galaxyproject/usegalaxy-playbook/commit/20a0676a81a8504a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: A files/galaxy/common/static/welcome_img/CARTGalaxy.png A files/galaxy/common/static/welcome_img/GAMe2017.png A files/galaxy/common/static/welcome_img/GAT2016OntimeReg.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation on landing page.

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[galaxyproject/galaxy] 56721e: Initial docstring linting.
by GitHub 06 Oct '16

06 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56721e7a0fe67e9aba55d4b52d97601b75b2beb9 https://github.com/galaxyproject/galaxy/commit/56721e7a0fe67e9aba55d4b52d97… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .travis.yml M lib/galaxy/util/__init__.py M setup.cfg M tox.ini Log Message: ----------- Initial docstring linting. - Apply one docstring lint to the global lint list (D302 - unicode docstrings should start with u"""). - Create an inclusion list with many more docstring checks (public modules need a docstring, white space and quoting issue, check imperative mood and capitializaton). Add a couple modules to this inclusion list. - Add tox and Travis targets for this linting. This gives a person who wants to work on improving Galaxy's in-code docstring documentation three ways to "raise the bar" for the project. One could: - Add more modules to the inclusion list (.ci/flake8_docstrings_include_list.txt). Many more modules should contain docstrings - especially things in galaxy-lib and web controllers. - Add more checks to the existing inclusion list checks - I'd say D101 and/or D103 first or any of the missing D2XX or D4XX options. D102 seems a bit too ambitious and I worry it'd be too much of a burden. - Pick some DXXX check that is ignored globally and fix it for the whole project and then remove it from the exclude list in setup.cfg. Commit: 9ae35cb64a57a67976459de1a9c589f3b70ab3f1 https://github.com/galaxyproject/galaxy/commit/9ae35cb64a57a67976459de1a9c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M tox.ini Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: 51aa341fe5ac7859233081af3ce5fab934349b1c https://github.com/galaxyproject/galaxy/commit/51aa341fe5ac7859233081af3ce5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .travis.yml M lib/galaxy/util/__init__.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #3004 from jmchilton/docstring_lint Initial docstring linting. Compare: https://github.com/galaxyproject/galaxy/compare/59a6d07b7b02...51aa341fe5ac

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[galaxyproject/galaxy] d7ab1c: UI, Modal: re-build dom on render
by GitHub 06 Oct '16

06 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: aa2e7834f697f02ebf11545b53882baee8b87f4e https://github.com/galaxyproject/galaxy/commit/aa2e7834f697f02ebf11545b5388… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix optional flag for library datasets in legacy library ui Commit: 26d381c9a5d77ecfa6bf3e96b2cb77df3d3f846d https://github.com/galaxyproject/galaxy/commit/26d381c9a5d77ecfa6bf3e96b2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #2962 from guerler/fix_library_optional_flag [16.07] Fix optional flag for library datasets in legacy library ui Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Commit: 375ed8cc81590a18a52b61e32307562488fd551e https://github.com/galaxyproject/galaxy/commit/375ed8cc81590a18a52b61e32307… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- polish resolvers section in conda faq docs Commit: ba274e37f2f0e8c9973b19c46fe99c5565c5118c https://github.com/galaxyproject/galaxy/commit/ba274e37f2f0e8c9973b19c46fe9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- describe the conda installation behavior a bit better Commit: 2899372791fdbba4f8db7c414a5447cf049987f3 https://github.com/galaxyproject/galaxy/commit/2899372791fdbba4f8db7c414a54… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update conda_faq.rst Commit: fdfe9d8c20a63e6e6e6951d5fe5cbd7d74446d0a https://github.com/galaxyproject/galaxy/commit/fdfe9d8c20a63e6e6e6951d5fe5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #19 from martenson/nsoranzo-patch-1-1 Small fixes to conda_faq.rst changes Commit: d9fab3345856770a16a98f18cf9e6185a4eae91a https://github.com/galaxyproject/galaxy/commit/d9fab3345856770a16a98f18cf9e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2998 from martenson/conda-faq-polish [16.07] Conda FAQ polish Commit: 1e8337df5a4acf9e899adc07883f967973cbcac7 https://github.com/galaxyproject/galaxy/commit/1e8337df5a4acf9e899adc07883f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix setting conda_copy_dependencies in galaxy.ini. (cherry picked from commit 9246b8629c3831ab623983c9003c4e92cbde97d5) Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 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: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d6845c249466d013b58ab021540fc5176096aaa0 https://github.com/galaxyproject/galaxy/commit/d6845c249466d013b58ab021540f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: f32b6446a7a4fd5a0bca2fa8e93d4407e0ce3938 https://github.com/galaxyproject/galaxy/commit/f32b6446a7a4fd5a0bca2fa8e93d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3008 from natefoo/conda-copy-dependencies [16.07] Fix setting conda_copy_dependencies in galaxy.ini. Commit: a2ee8d10af84332bf1afa1e32f0acf9cdb754f0a https://github.com/galaxyproject/galaxy/commit/a2ee8d10af84332bf1afa1e32f0a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: doc/source/admin/conda_faq.rst static/maps/mvc/ui/ui-modal.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-modal.js Commit: 59a6d07b7b02f2b23719acdc83122eae89e49b78 https://github.com/galaxyproject/galaxy/commit/59a6d07b7b02f2b23719acdc8312… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #3010 from nsoranzo/merge_release_16.07 Merge release_16.07 into dev Compare: https://github.com/galaxyproject/galaxy/compare/c03748dd49c0...59a6d07b7b02

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[galaxyproject/galaxy] 2b9034: Update some old information in API guideline docs.
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b9034d597941ad055975fb776506b8de2382c67 https://github.com/galaxyproject/galaxy/commit/2b9034d597941ad055975fb77650… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Update some old information in API guideline docs. Commit: c03748dd49c060a68d07bce56eae33e0ba154414 https://github.com/galaxyproject/galaxy/commit/c03748dd49c060a68d07bce56eae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Merge pull request #3011 from jmchilton/api_docs Update some old information in API guideline docs. Compare: https://github.com/galaxyproject/galaxy/compare/16c2227b9315...c03748dd49c0

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[galaxyproject/infrastructure-playbook] 1d98b2: Install tmpwatch on Jetstream controllers
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1d98b22aa0f5882a450039c99e66396cb7f5923c https://github.com/galaxyproject/infrastructure-playbook/commit/1d98b22aa0f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Install tmpwatch on Jetstream controllers Commit: fe8dd0d9b8659ab0e793664ffd078bdcdec4c592 https://github.com/galaxyproject/infrastructure-playbook/commit/fe8dd0d9b86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Schedule scratch cleaning cron jobs on Jetstream controllers Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/95e35c8576…

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[galaxyproject/galaxy] 1e8337: Fix setting conda_copy_dependencies in galaxy.ini.
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 1e8337df5a4acf9e899adc07883f967973cbcac7 https://github.com/galaxyproject/galaxy/commit/1e8337df5a4acf9e899adc07883f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix setting conda_copy_dependencies in galaxy.ini. (cherry picked from commit 9246b8629c3831ab623983c9003c4e92cbde97d5) Commit: f32b6446a7a4fd5a0bca2fa8e93d4407e0ce3938 https://github.com/galaxyproject/galaxy/commit/f32b6446a7a4fd5a0bca2fa8e93d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3008 from natefoo/conda-copy-dependencies [16.07] Fix setting conda_copy_dependencies in galaxy.ini. Compare: https://github.com/galaxyproject/galaxy/compare/d6845c249466...f32b6446a7a4

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[galaxyproject/galaxy] 6d27a3: Fix initial conda version at 4.0.5
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 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: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d6845c249466d013b58ab021540fc5176096aaa0 https://github.com/galaxyproject/galaxy/commit/d6845c249466d013b58ab021540f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/d9fab3345856...d6845c249466

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galaxy-commits October 2016