Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e0... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb06... Author: carlfeberhard <carlfeberhard@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: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf4923... Author: Dave B <dave@bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe567... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c9... Author: carlfeberhard <carlfeberhard@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/aa2e7834f697f02ebf11545b53882... Author: guerler <aysam.guerler@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: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e043... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341ddc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71ca... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a53743456865813... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca23567... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 26d381c9a5d77ecfa6bf3e96b2cb77df3d3f846d https://github.com/galaxyproject/galaxy/commit/26d381c9a5d77ecfa6bf3e96b2cb7... Author: John Chilton <jmchilton@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/e667f9f360388839d723421b88483... Author: John Chilton <jmchilton@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/04d62e242412d0eb6e739f3577256... Author: Martin Cech <cech.marten@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/375ed8cc81590a18a52b61e323075... Author: Martin Cech <cech.marten@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/ba274e37f2f0e8c9973b19c46fe99... Author: Martin Cech <cech.marten@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/2899372791fdbba4f8db7c414a544... Author: Nicola Soranzo <nsoranzo@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/fdfe9d8c20a63e6e6e6951d5fe5cb... Author: Martin Cech <cech.marten@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/d9fab3345856770a16a98f18cf9e6... Author: Nicola Soranzo <nsoranzo@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/1e8337df5a4acf9e899adc07883f9... Author: John Chilton <jmchilton@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/6d27a3c4b6184b393e535afd32f87... Author: Marius van den Beek <m.vandenbeek@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#L61) and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f55271... Author: Björn Grüning <bjoern@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/224c2126c73617ec906abc1e08d5f... Author: Nicola Soranzo <nicola.soranzo@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/d6845c249466d013b58ab021540fc... Author: Nicola Soranzo <nicola.soranzo@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/f32b6446a7a4fd5a0bca2fa8e93d4... Author: John Chilton <jmchilton@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: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda87335... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b631... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d71... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e5... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 735c682ead5f97ef150632b3ecc4d8d9bd593a33 https://github.com/galaxyproject/galaxy/commit/735c682ead5f97ef150632b3ecc4d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M scripts/tool_shed/build_ts_whoosh_index.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 M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #3037 from galaxyproject/release_16.07 [master-toolshed] merge-in release_16.07 changes Compare: https://github.com/galaxyproject/galaxy/compare/673a9a3a5b55...735c682ead5f