September 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 7d2cd2: replace colon and comma in role names since they a...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d2cd2272299b94b01c8d22c0c1f7f5cbfb2b91a https://github.com/galaxyproject/galaxy/commit/7d2cd2272299b94b01c8d22c0c1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- replace colon and comma in role names since they are also separators Commit: 3b4bd3bb6fa922c9e2156fe87660de409acf3367 https://github.com/galaxyproject/galaxy/commit/3b4bd3bb6fa922c9e2156fe87660… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- make client Commit: 153dfaa68080481607a90731c5a0825754cf713d https://github.com/galaxyproject/galaxy/commit/153dfaa68080481607a90731c5a0… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Merge pull request #4621 from martenson/library-sharing-roles replace separators in library sharing role names Compare: https://github.com/galaxyproject/galaxy/compare/ea7b27443715...153dfaa68080

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[galaxyproject/galaxy] 860f0a: Some function description updates
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 860f0ab6ba6c45c98b5c9f3f002096cc9ef0c7b6 https://github.com/galaxyproject/galaxy/commit/860f0ab6ba6c45c98b5c9f3f0020… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Some function description updates Commit: e3e26ae202369876eb1523562b2582f2a15495cb https://github.com/galaxyproject/galaxy/commit/e3e26ae202369876eb1523562b25… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Updated a comment Commit: 3cca06a153253f65f752d1f80aae2fd2e3cf221e https://github.com/galaxyproject/galaxy/commit/3cca06a153253f65f752d1f80aae… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- updated a comment. Commit: 604fdde4248dc2d7f261e63449ab5530463058a3 https://github.com/galaxyproject/galaxy/commit/604fdde4248dc2d7f261e63449ab… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- typo Commit: ea7b27443715730597e273b315dce875910738ce https://github.com/galaxyproject/galaxy/commit/ea7b27443715730597e273b315dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4629 from VJalili/patch-3 Updated function description and fix some typos Compare: https://github.com/galaxyproject/galaxy/compare/fe88dab79b0b...ea7b27443715

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[galaxyproject/galaxy] 69af37: Typo fix
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69af37f653569117371413bfadd06e5428486526 https://github.com/galaxyproject/galaxy/commit/69af37f653569117371413bfadd0… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Typo fix Commit: fe88dab79b0b47245c079ebc372563392c917f30 https://github.com/galaxyproject/galaxy/commit/fe88dab79b0b47245c079ebc3725… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #4628 from VJalili/patch-3 Typo fix Compare: https://github.com/galaxyproject/galaxy/compare/540322e38856...fe88dab79b0b

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[galaxyproject/galaxy] 1c1ca9: Fix loose->lose in help text for library dataset v...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c1ca9bd91298e2265cb4a9e6982f18c3e4ae39d https://github.com/galaxyproject/galaxy/commit/1c1ca9bd91298e2265cb4a9e6982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Fix loose->lose in help text for library dataset view. Commit: d5aba7da15f5a05821e7659828bd701fd438769e https://github.com/galaxyproject/galaxy/commit/d5aba7da15f5a05821e7659828bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Three more looses. Commit: 7831b9889897e1d51ba2004cc8fcc5df079c0594 https://github.com/galaxyproject/galaxy/commit/7831b9889897e1d51ba2004cc8fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Occurred, spelling. Commit: 0ea6272f5d35a769bc63a4706c503793fa903fe2 https://github.com/galaxyproject/galaxy/commit/0ea6272f5d35a769bc63a4706c50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- More spelling. Commit: 540322e38856cc86a4a3d91aa3ac670418378d90 https://github.com/galaxyproject/galaxy/commit/540322e38856cc86a4a3d91aa3ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- Merge pull request #4626 from dannon/loose_use Misc. spelling/grammatical error fixes. Compare: https://github.com/galaxyproject/galaxy/compare/64af1bd9e962...540322e38856

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[galaxyproject/galaxy] fc90ae: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Commit: 64af1bd9e96265cbd6b21faadbad5adea4a2d613 https://github.com/galaxyproject/galaxy/commit/64af1bd9e96265cbd6b21faadbad… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c5ff555ec4ef...64af1bd9e962

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[galaxyproject/galaxy] 6c6c80: When a page is involved, the ID will be wrong
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Commit: 685b9de09bca5a2973de336b93865273c9fa975c https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b9386… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 759780b72c03efd6563c0c53efc9edff9505979c https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 41fe55129a3af95d7ef84ecb387b954b14509843 https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: lib/galaxy/datatypes/data.py Commit: b17fbfb968b8921729798c909220e522abfb29fd https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix startup of galaxy when wehbooks dir is empty Reported by @alpapan on gitter. Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4 https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae7… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge pull request #4570 from mvdbeek/webhook_loading_fix [17.05] Bug: Fix startup of galaxy when wehbooks dir is empty Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Commit: a9facdc7568f68af06ba7474611feeeabf60466b https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 83b363d5207625b916523b7d08b4fff26e8379ed https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/datatypes_conf.xml.sample M create_db.sh M extract_dataset_parts.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-select-content.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/base/controlled-fetch-collection.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' Compare: https://github.com/galaxyproject/galaxy/compare/4a7045c8d210...0a39bfcbf7dc

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[galaxyproject/galaxy] fc90ae: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Compare: https://github.com/galaxyproject/galaxy/compare/83b363d52076...97e8e3618531

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[galaxyproject/galaxy] d8dfbe: unify library dataset permission frontend for all...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8dfbe56c427e73f359595609c932105114950eb https://github.com/galaxyproject/galaxy/commit/d8dfbe56c427e73f359595609c93… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- unify library dataset permission frontend for all users also refactor Commit: 028aac0a3dabe31a5392feaf35a93900ac7eb8b7 https://github.com/galaxyproject/galaxy/commit/028aac0a3dabe31a5392feaf35a9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- respect expose_user_email when offering roles to datalib permissions Commit: a1cd3bd1e41d4da17d116c1a8cde1eedb6143ab9 https://github.com/galaxyproject/galaxy/commit/a1cd3bd1e41d4da17d116c1a8cde… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- rebuild client Commit: 1b2221cd5600823285737fae5d7819c3f2670cfb https://github.com/galaxyproject/galaxy/commit/1b2221cd5600823285737fae5d78… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix indent Commit: 9084edd8200cc7c7387d62ae969921daf3feec86 https://github.com/galaxyproject/galaxy/commit/9084edd8200cc7c7387d62ae9699… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- fix typo thanks @dannon Commit: c5ff555ec4ef32e0d12020c4ea4e0f52f214e31e https://github.com/galaxyproject/galaxy/commit/c5ff555ec4ef32e0d12020c4ea4e… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Merge pull request #4611 from martenson/respect-email-exposure respect expose_user_email configuration in datalibraries permissions list Compare: https://github.com/galaxyproject/galaxy/compare/c677621481ab...c5ff555ec4ef

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[galaxyproject/galaxy] d6ae91: Fix group creation label in admin panel
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6ae9127ebb7c654ea93f98b1de18ccb92705713 https://github.com/galaxyproject/galaxy/commit/d6ae9127ebb7c654ea93f98b1de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix group creation label in admin panel Commit: d247d698a29e3e24816068624061411be97d6ad1 https://github.com/galaxyproject/galaxy/commit/d247d698a29e3e24816068624061… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix auto create checkbox name Commit: c677621481abf7823f2d77a506c8aa6908070022 https://github.com/galaxyproject/galaxy/commit/c677621481abf7823f2d77a506c8… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #4619 from guerler/fix_group_label Fix group creation label in admin panel and checkbox name Compare: https://github.com/galaxyproject/galaxy/compare/90eed104f0d8...c677621481ab

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[galaxyproject/galaxy] e1be66: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1be66312b536a419383746b8e702b6148edeeec https://github.com/galaxyproject/galaxy/commit/e1be66312b536a419383746b8e70… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 90eed104f0d80fed13ac6b5cfc13f96d28d01771 https://github.com/galaxyproject/galaxy/commit/90eed104f0d80fed13ac6b5cfc13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4616 from nsoranzo/fix_scripts Fix virtualenv activation for some scripts Compare: https://github.com/galaxyproject/galaxy/compare/8b9e91310fd9...90eed104f0d8

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