March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] dd67ca: Ignore tool xml datatype settings for dragged hist...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd67cac5d5baaedff0b3bde8be1fc136eddefe79 https://github.com/galaxyproject/galaxy/commit/dd67cac5d5baaedff0b3bde8be1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Ignore tool xml datatype settings for dragged history items Commit: abf6be7e6441f0bb62861c3da0d7f624077b17d0 https://github.com/galaxyproject/galaxy/commit/abf6be7e6441f0bb62861c3da0d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove debug statements, use drop data where needed Commit: 8412a725c48a24db3345826be32cc2c86d3726fe https://github.com/galaxyproject/galaxy/commit/8412a725c48a24db3345826be32c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Validate type using collection, from @jmchilton Commit: 83adfc6ef64e1da0dd64d64b4b9a0236bef12b94 https://github.com/galaxyproject/galaxy/commit/83adfc6ef64e1da0dd64d64b4b9a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add source to data entry Commit: 617e3db5487373005531a5c068c47f7fc89a4d18 https://github.com/galaxyproject/galaxy/commit/617e3db5487373005531a5c068c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add additional check for history items Commit: 11b32f38f46cbdaf78e0b1bfa9d14c8e6d1a6068 https://github.com/galaxyproject/galaxy/commit/11b32f38f46cbdaf78e0b1bfa9d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #5657 from guerler/disable_drop_validation Disable tool input datatype validation for dropped history items Compare: https://github.com/galaxyproject/galaxy/compare/8316cb64b289...11b32f38f46c

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[galaxyproject/galaxy] e310d7: improve galaxy update commands, update some checkp...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e310d7a1f0f47e992eb1ac99ebcfafce0c72cb3d https://github.com/galaxyproject/galaxy/commit/e310d7a1f0f47e992eb1ac99ebcf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- improve galaxy update commands, update some checkpoints Commit: b2d7ca40d3753d95e4d1d7c3e49e6d425e3328b1 https://github.com/galaxyproject/galaxy/commit/b2d7ca40d3753d95e4d1d7c3e49e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix typo Commit: 8316cb64b28937f3a821088812c8055b3b218274 https://github.com/galaxyproject/galaxy/commit/8316cb64b28937f3a821088812c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #5731 from martenson/botstrapdev improve galaxy update commands, update some bootstrap checkpoints Compare: https://github.com/galaxyproject/galaxy/compare/0cf88623ee36...8316cb64b289

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[galaxyproject/galaxy] ef45ae: Upgrade clone failure logging to error
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ef45ae3752a4ea4da73719e2917a064c8e239ab3 https://github.com/galaxyproject/galaxy/commit/ef45ae3752a4ea4da73719e2917a… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Upgrade clone failure logging to error When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'. Commit: a73a1d6250373cd1e6bb1255052ee7cb541e4569 https://github.com/galaxyproject/galaxy/commit/a73a1d6250373cd1e6bb1255052e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5728 from mvdbeek/backport_logging_level_change [18.01] Backport 5724: upgrade clone failure logging to error Compare: https://github.com/galaxyproject/galaxy/compare/240f14d62fb6...a73a1d625037

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[galaxyproject/galaxy] 50035b: improve update commands in RN, clarify uwsgi confi...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 50035b184e0ceba61f21f223e5f701710dd86d19 https://github.com/galaxyproject/galaxy/commit/50035b184e0ceba61f21f223e5f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- improve update commands in RN, clarify uwsgi config changes Commit: 924eecc67a3155578aea6a484d9bfd86d0cc5aba https://github.com/galaxyproject/galaxy/commit/924eecc67a3155578aea6a484d9b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Add missing `.` Commit: 3699e9e4919dcb727af3ff0e7457794642973dfa https://github.com/galaxyproject/galaxy/commit/3699e9e4919dcb727af3ff0e7457… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- re-add the motivation for uwsgi switch Commit: 240f14d62fb6bdbf02f51ff1af19602494560880 https://github.com/galaxyproject/galaxy/commit/240f14d62fb6bdbf02f51ff1af19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5730 from martenson/bootstrap [18.01] improve update commands in RN, clarify uwsgi config changes Compare: https://github.com/galaxyproject/galaxy/compare/74d0bcb353b4...240f14d62fb6

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[galaxyproject/usegalaxy-playbook] 99b843: Update htseq-count
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 99b84394a10ef5ca04c1213b0f4c3bea76797d42 https://github.com/galaxyproject/usegalaxy-playbook/commit/99b84394a10ef5ca… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update htseq-count

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[galaxyproject/galaxy] ebb7be: Merge pull request #5688 from martenson/security-r...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e57… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5688 from martenson/security-rn [18.01] backport add security announcement to the release notes Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754 https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999 https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type [18.01] Fix/default role type on auto created roles Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55 https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Clarfify that nginx-extras needs to be install for the upload_store directive to work Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #5717 from mvdbeek/nginx_doc_update [18.01] Clarify that nginx-extras needs to be install for the upload_store d… Commit: 3b87dac78028846a803e33ae13199535c70f567d https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae1319… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Add Galaxy `lib` directory to Python path for 2 scripts Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e . Fix https://github.com/galaxyproject/galaxy/issues/5722 . Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009 https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts [17.09] Add Galaxy `lib` directory to Python path for 2 scripts Commit: 74d0bcb353b4824d4d4af9ffe6bd909924feca62 https://github.com/galaxyproject/galaxy/commit/74d0bcb353b4824d4d4af9ffe6bd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 0cf88623ee3648a36ba6fd8c9be23fb07d9fc4ac https://github.com/galaxyproject/galaxy/commit/0cf88623ee3648a36ba6fd8c9be2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md M lib/galaxy/security/__init__.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/66ce5ec83332...0cf88623ee36

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[galaxyproject/galaxy] 3b87da: Add Galaxy `lib` directory to Python path for 2 sc...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 3b87dac78028846a803e33ae13199535c70f567d https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae1319… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Add Galaxy `lib` directory to Python path for 2 scripts Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e . Fix https://github.com/galaxyproject/galaxy/issues/5722 . Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009 https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts [17.09] Add Galaxy `lib` directory to Python path for 2 scripts Commit: 74d0bcb353b4824d4d4af9ffe6bd909924feca62 https://github.com/galaxyproject/galaxy/commit/74d0bcb353b4824d4d4af9ffe6bd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/127d7b8c3c85...74d0bcb353b4

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[galaxyproject/galaxy] 3b87da: Add Galaxy `lib` directory to Python path for 2 sc...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 3b87dac78028846a803e33ae13199535c70f567d https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae1319… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Add Galaxy `lib` directory to Python path for 2 scripts Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e . Fix https://github.com/galaxyproject/galaxy/issues/5722 . Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009 https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts [17.09] Add Galaxy `lib` directory to Python path for 2 scripts Compare: https://github.com/galaxyproject/galaxy/compare/f8d44c2b6951...5dcd9ed0255c

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[galaxyproject/galaxy] b1ad0e: Upgrade clone failure logging to error
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1ad0e78fa0da0b56d75d9921d799226f373f74a https://github.com/galaxyproject/galaxy/commit/b1ad0e78fa0da0b56d75d9921d79… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Upgrade clone failure logging to error When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'. Commit: 66ce5ec83332aaf5cb393fea6b4d7e9ad60471d0 https://github.com/galaxyproject/galaxy/commit/66ce5ec83332aaf5cb393fea6b4d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5724 from pvanheus/patch-1 Upgrade clone failure logging to error Compare: https://github.com/galaxyproject/galaxy/compare/ac3a0cbdc58f...66ce5ec83332

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[galaxyproject/galaxy] ef6f7f: Memory usage bug fixes and code cleanup/simplifica...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef6f7f62ab679928045c816a3cb719fb3bcea507 https://github.com/galaxyproject/galaxy/commit/ef6f7f62ab679928045c816a3cb7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/checkers.py M lib/galaxy_ext/metadata/set_metadata.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Memory usage bug fixes and code cleanup/simplification for upload tool Commit: da24d9106db1051a82c7814e847b679bac01d71c https://github.com/galaxyproject/galaxy/commit/da24d9106db1051a82c7814e847b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Fixes for changes to checkers.check_zip Commit: 0163a57f0ed562a7c699c6121a8bec87cd4016ea https://github.com/galaxyproject/galaxy/commit/0163a57f0ed562a7c699c6121a8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M tools/data_source/upload.py Log Message: ----------- Additional fixes for failing tests Commit: 2dc5cb7f47a50a0b3c79f6da1bf1b6bc08744a86 https://github.com/galaxyproject/galaxy/commit/2dc5cb7f47a50a0b3c79f6da1bf1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix linting errors Commit: 82408eb179a482a9e24b74d0658b89df3f87f354 https://github.com/galaxyproject/galaxy/commit/82408eb179a482a9e24b74d0658b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- I wanted to make sure that umask was still being respected with the changes to the upload tool - it is, but there were a few places that it could be missed, so I added these. Commit: 11917108f3b4b94855453d308cbfd0649c593400 https://github.com/galaxyproject/galaxy/commit/11917108f3b4b94855453d308cbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Improve extension stripping Commit: ac3a0cbdc58fbefc344b16aeac6a0d238a792fa0 https://github.com/galaxyproject/galaxy/commit/ac3a0cbdc58fbefc344b16aeac6a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/checkers.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5689 from natefoo/upload-memfix Memory and performance fixes for upload tool Compare: https://github.com/galaxyproject/galaxy/compare/dbf6f5825171...ac3a0cbdc58f

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