- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] f61a0a: Update TTS
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f61a0acbc72a25dd139c8539d3dbe03d1f99089b https://github.com/galaxyproject/usegalaxy-playbook/commit/f61a0acbc72a25dd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS

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[galaxyproject/galaxy] 007ae8: Default slow request tracking to disabled; this is...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 007ae8f9377666ab84599aee20fce2a63cc03fbc https://github.com/galaxyproject/galaxy/commit/007ae8f9377666ab84599aee20fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Default slow request tracking to disabled; this is only used in Galaxy and should fix TS/reports error. Commit: 39fd5fdc05e81918df322d1b84b444864d67174d https://github.com/galaxyproject/galaxy/commit/39fd5fdc05e81918df322d1b84b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #5513 from dannon/fix_non_gxy_sentry_middleware Default slow request tracking to disabled; Compare: https://github.com/galaxyproject/galaxy/compare/201d76568f75...39fd5fdc05e8

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[galaxyproject/usegalaxy-playbook] b42b6c: Update TTS
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b42b6cf629469395641cde0566fc359965411129 https://github.com/galaxyproject/usegalaxy-playbook/commit/b42b6cf629469395… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS

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[galaxyproject/galaxy] 7feef3: Fix "Go back to workflows list" link on workflow s...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7feef3dc0e6853fb3a0ded2056f39d1ff0f222e8 https://github.com/galaxyproject/galaxy/commit/7feef3dc0e6853fb3a0ded2056f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix "Go back to workflows list" link on workflow sharing interface. Commit: 9df2813524275b89e97f9dd6b8d4ae4e4b307947 https://github.com/galaxyproject/galaxy/commit/9df2813524275b89e97f9dd6b8d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix more workflow sharing broken links Commit: c5568a7b1ac07dd86f45801c2706173701b20dc2 https://github.com/galaxyproject/galaxy/commit/c5568a7b1ac07dd86f45801c2706… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #5467 from dannon/workflow_sharing_link_fixes [18.01] Workflow sharing link fixes Commit: ba3b3d5c180e318c26c8db7f0dff7f26115554df https://github.com/galaxyproject/galaxy/commit/ba3b3d5c180e318c26c8db7f0dff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- do not allow codefiles for TS tool loading Commit: aefe0e14498d5e5bf5c5f9307ab28f05d0efb81c https://github.com/galaxyproject/galaxy/commit/aefe0e14498d5e5bf5c5f9307ab2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge pull request #5510 from martenson/ts-deny-codefile [18.01] do not allow codefiles for TS tool loading Commit: 201d76568f75eeeebde3b9e585f54dd14332fca7 https://github.com/galaxyproject/galaxy/commit/201d76568f75eeeebde3b9e585f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M templates/webapps/galaxy/workflow/sharing.mako M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e58aaef95997...201d76568f75

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[galaxyproject/galaxy] ba3b3d: do not allow codefiles for TS tool loading
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ba3b3d5c180e318c26c8db7f0dff7f26115554df https://github.com/galaxyproject/galaxy/commit/ba3b3d5c180e318c26c8db7f0dff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- do not allow codefiles for TS tool loading Commit: aefe0e14498d5e5bf5c5f9307ab28f05d0efb81c https://github.com/galaxyproject/galaxy/commit/aefe0e14498d5e5bf5c5f9307ab2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge pull request #5510 from martenson/ts-deny-codefile [18.01] do not allow codefiles for TS tool loading Compare: https://github.com/galaxyproject/galaxy/compare/c5568a7b1ac0...aefe0e14498d

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[galaxyproject/usegalaxy-playbook] e3fe36: Disable conda dependency copying, set conda_prefix...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e3fe36236f7687aab52b55fb78c699557866f3ee https://github.com/galaxyproject/usegalaxy-playbook/commit/e3fe36236f7687aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable conda dependency copying, set conda_prefix to CVMFS

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[galaxyproject/galaxy] e13740: Drop short-lived 'make client-production' warning ...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e13740a3f6f91a86af0b19ce5121b4bd7f628182 https://github.com/galaxyproject/galaxy/commit/e13740a3f6f91a86af0b19ce5121… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M Makefile Log Message: ----------- Drop short-lived 'make client-production' warning from build scripts, since we're not including these moving forward. Commit: e58aaef95997f37974a501e69c4c00fba80d72e8 https://github.com/galaxyproject/galaxy/commit/e58aaef95997f37974a501e69c4c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5508 from dannon/no-more-client-commits Drop short-lived 'make client-production' warning from build scripts,… Compare: https://github.com/galaxyproject/galaxy/compare/6d00958d43ea...e58aaef95997

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[galaxyproject/usegalaxy-playbook] d29f0a: Temp fix for weird Main installer issue not being ...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d29f0adfce53375e9f9b4abaaacf04b80597bc9f https://github.com/galaxyproject/usegalaxy-playbook/commit/d29f0adfce53375e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/main/group_vars/dbservers/vault.yml Log Message: ----------- Temp fix for weird Main installer issue not being able to connect to the template1 database.

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[galaxyproject/usegalaxy-playbook] fc68d3: Increase AMQP acknowledgement republish time to 5 ...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fc68d39125ded0a2109b4e2aa06966e7560e2f83 https://github.com/galaxyproject/usegalaxy-playbook/commit/fc68d39125ded0a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase AMQP acknowledgement republish time to 5 minutes

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[galaxyproject/galaxy] b114f3: Add tool that tags collection elements from a file
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b114f3f7b9d483509e7d684aa8be54e769fddbf7 https://github.com/galaxyproject/galaxy/commit/b114f3f7b9d483509e7d684aa8be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt Log Message: ----------- Add tool that tags collection elements from a file This tags collection elements (but not collections). Commit: b2be7b51814a4354307e8f0a0df0c8885ef73bb0 https://github.com/galaxyproject/galaxy/commit/b2be7b51814a4354307e8f0a0df0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/managers/taggable.py Log Message: ----------- Sort tags when serializing them Commit: f9664a0863b24ff738aefcbe520f033e5f53e76d https://github.com/galaxyproject/galaxy/commit/f9664a0863b24ff738aefcbe520f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/base/interactor.py Log Message: ----------- Make presence of tags testable Commit: fd373501c78dee268844e82fa1a56a108d34cf23 https://github.com/galaxyproject/galaxy/commit/fd373501c78dee268844e82fa1a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add tag from file tool to samples_tool_conf.xml Commit: e306a447c080f8d252a9a7fe49f4d36f6a8de4a9 https://github.com/galaxyproject/galaxy/commit/e306a447c080f8d252a9a7fe49f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/tag_collection_from_file.xml Log Message: ----------- Switch tag tool to use select and add remove mode Commit: d14bae73f72cd454ef41bb1815cf1dfc9256db5d https://github.com/galaxyproject/galaxy/commit/d14bae73f72cd454ef41bb1815cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/tools/tag_collection_from_file.xml M test-data/new_tags_1.txt Log Message: ----------- Flush once per tag Not sure this is the right thing to do (maybe there is a better way to get an ID?), but it avoids ``` IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" DETAIL: Key (name)=(group) already exists. [SQL: 'INSERT INTO tag (type, parent_id, name) VALUES (%(type)s, %(parent_id)s, %(name)s) RETURNING tag.id'] [parameters: {'parent_id': None, 'type': 0, 'name': u'group'}] galaxy.tools.execute WARNING 2018-02-06 15:22:38,808 [p:2122,w:1,m:0] [uWSGIWorker1Core1] There was a failure executing a job for tool [__TAG_FROM_FILE__] - Error executing tool: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" ``` Commit: 6d00958d43eab15bf2c94bc9088dfa5f162ce3c9 https://github.com/galaxyproject/galaxy/commit/6d00958d43eab15bf2c94bc9088d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5462 from mvdbeek/tag_collection_from_files Tool that adds/sets tags for collection elements from a file Compare: https://github.com/galaxyproject/galaxy/compare/0367a356d528...6d00958d43ea

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[galaxyproject/galaxy] 3ae47e: Merge remote-tracking branch 'galaxyproject/dev' i...
by GitHub 11 Feb '18

11 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ae47e611d2582c543d42a69d0c320634a70150f https://github.com/galaxyproject/galaxy/commit/3ae47e611d2582c543d42a69d0c3… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh R 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templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/user/api_keys.mako R templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/user/manage_info.mako R templates/webapps/galaxy/visualization/create.mako M templates/webapps/galaxy/visualization/display.mako R templates/webapps/galaxy/visualization/list.mako R templates/webapps/galaxy/visualization/list_published.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako R templates/webapps/galaxy/workflow/configure_menu.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako R templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/reports/base_panels.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/center.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako R templates/webapps/tool_shed/repository/grid.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A templates/webapps/tool_shed/user/username.mako M test-data/1.fastqsanger A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test-data/1.fastqsolexa A test-data/1.sam.gz A test-data/5_Ig-like.gff A test-data/bad.html.gz A test-data/bam_from_sam.bam A test-data/bam_native_from_sam.bam A test-data/filter_labels_1.txt A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test-data/neostore.zip A test-data/new_element_sort_order.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt A test-data/random-file A test-data/sam_with_header.sam Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: 007e3cc2db247096cf06b59d4c7583112dacd7fa https://github.com/galaxyproject/galaxy/commit/007e3cc2db247096cf06b59d4c75… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Add Proteomics datatypes proBAM and proBED Add datatypes proBAM and proBED for genomic alignment and annotation of proteomic analysis results. Commit: 0367a356d528b3ca395eec1f3de57563cba19c2e https://github.com/galaxyproject/galaxy/commit/0367a356d528b3ca395eec1f3de5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #5360 from jj-umn/dev Add Proteomics datatypes proBAM and proBED Compare: https://github.com/galaxyproject/galaxy/compare/587f20cf9c0b...0367a356d528

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[galaxyproject/galaxy] 7feef3: Fix "Go back to workflows list" link on workflow s...
by GitHub 11 Feb '18

11 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7feef3dc0e6853fb3a0ded2056f39d1ff0f222e8 https://github.com/galaxyproject/galaxy/commit/7feef3dc0e6853fb3a0ded2056f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix "Go back to workflows list" link on workflow sharing interface. Commit: 9df2813524275b89e97f9dd6b8d4ae4e4b307947 https://github.com/galaxyproject/galaxy/commit/9df2813524275b89e97f9dd6b8d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix more workflow sharing broken links Commit: c5568a7b1ac07dd86f45801c2706173701b20dc2 https://github.com/galaxyproject/galaxy/commit/c5568a7b1ac07dd86f45801c2706… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #5467 from dannon/workflow_sharing_link_fixes [18.01] Workflow sharing link fixes Compare: https://github.com/galaxyproject/galaxy/compare/d91078024bf3...c5568a7b1ac0

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[galaxyproject/galaxy] 29acb1: Show parameter name in DataToolParameter exception
by GitHub 11 Feb '18

11 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29acb11df5c971a2bc99ae534e36cffa046e2a6c https://github.com/galaxyproject/galaxy/commit/29acb11df5c971a2bc99ae534e36… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Show parameter name in DataToolParameter exception Goal is to replace this kind of output in a failed test run: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build. with: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build in parameter 'XXX'. Commit: 587f20cf9c0b6d250bee403cf3baab85e1272dcf https://github.com/galaxyproject/galaxy/commit/587f20cf9c0b6d250bee403cf3ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #5465 from peterjc/patch-5 Show parameter name in DataToolParameter exception Compare: https://github.com/galaxyproject/galaxy/compare/d0b4503e0cc2...587f20cf9c0b

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[galaxyproject/ansible-galaxy] d94c2d: Fix pypi index url
by GitHub 09 Feb '18

09 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: d94c2de1a06782aebf88ebbc5c7e0533bd326f09 https://github.com/galaxyproject/ansible-galaxy/commit/d94c2de1a06782aebf88… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Fix pypi index url ping @drosofff, who asked about this on gitter. Commit: ec9cee294f060ef699929f52e848afbcdad899ee https://github.com/galaxyproject/ansible-galaxy/commit/ec9cee294f060ef69992… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Merge pull request #24 from mvdbeek/fix_pypi_url Fix pypi index url Compare: https://github.com/galaxyproject/ansible-galaxy/compare/6544db9b17cc...ec9c…

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[galaxyproject/galaxy] 1ea416: Python3: Update pulsar-galaxy-lib dependency to 0....
by GitHub 09 Feb '18

09 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ea41622632aeefdac7138ad515659a594887908 https://github.com/galaxyproject/galaxy/commit/1ea41622632aeefdac7138ad5156… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Commit: d0b4503e0cc2e3d083330da08672b6ca35d5c4b2 https://github.com/galaxyproject/galaxy/commit/d0b4503e0cc2e3d083330da08672… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5494 from nsoranzo/update_pulsar_galaxy_lib Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Compare: https://github.com/galaxyproject/galaxy/compare/b6fe83409ad5...d0b4503e0cc2

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[galaxyproject/galaxy] 6f2a0c: Unify config-rebuild Makefile targets
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f2a0cceb03b4277f9ed4e8761cc011e230fa08e https://github.com/galaxyproject/galaxy/commit/6f2a0cceb03b4277f9ed4e8761cc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Unify config-rebuild Makefile targets Rebuild reports sample and RST from schema with the new Makefile target. Commit: b6fe83409ad57e15adcb1b270102827e5e5fc084 https://github.com/galaxyproject/galaxy/commit/b6fe83409ad57e15adcb1b270102… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Merge pull request #5488 from nsoranzo/unify_makefile_targets Unify config-rebuild Makefile targets Compare: https://github.com/galaxyproject/galaxy/compare/10ff797ac77d...b6fe83409ad5

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[galaxyproject/usegalaxy-playbook]
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] 8a295a: Test mutable configs
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8a295a1cc22b41985a7b53cb30f0d21054e631b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/8a295a1cc22b4198… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: f361a5d29332e2f89cfbd0e7ed1e06678f41e8e5 https://github.com/galaxyproject/usegalaxy-playbook/commit/f361a5d29332e2f8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Commit: bbc4b2af277691f56ff4c5edfdb2c0f2592d97ae https://github.com/galaxyproject/usegalaxy-playbook/commit/bbc4b2af277691f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Enable slow request logging, update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a98c020ac2c8...…

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[galaxyproject/usegalaxy-playbook] 39dd10: enable gzipping on main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39dd104bc464869228dbc2afd85b9e829a345b33 https://github.com/galaxyproject/usegalaxy-playbook/commit/39dd104bc4648692… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- enable gzipping on main and unify the gzip_types with Test Commit: a98c020ac2c8a9e84228c05040d57555ec9ecafe https://github.com/galaxyproject/usegalaxy-playbook/commit/a98c020ac2c8a9e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- Merge pull request #91 from galaxyproject/martenson-patch-1 enable gzipping on main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/182fa5c14203...…

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[galaxyproject/usegalaxy-playbook] 39dd10: enable gzipping on main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39dd104bc464869228dbc2afd85b9e829a345b33 https://github.com/galaxyproject/usegalaxy-playbook/commit/39dd104bc4648692… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/webservers.yml Log Message: ----------- enable gzipping on main and unify the gzip_types with Test

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[galaxyproject/galaxy] b5945a: Add IdeasPre datatype subclassed from Rgenetics
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5945ad3e3a972acb41c87c2ddeeff222779020c https://github.com/galaxyproject/galaxy/commit/b5945ad3e3a972acb41c87c2ddee… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Add IdeasPre datatype subclassed from Rgenetics Commit: 3fdd4edc5c1954dc750dfeff03cb3205ee1b6042 https://github.com/galaxyproject/galaxy/commit/3fdd4edc5c1954dc750dfeff03cb… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Subclass IdeasPre from Html Commit: b463be78a5066c7e6c389c43af2bd863f05e4a80 https://github.com/galaxyproject/galaxy/commit/b463be78a5066c7e6c389c43af2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 977bbf1481b2fd36512f869c01f0af6ba4099a92 https://github.com/galaxyproject/galaxy/commit/977bbf1481b2fd36512f869c01f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: eba3fb4b35570fc704dbb9a70c733293a2ee4514 https://github.com/galaxyproject/galaxy/commit/eba3fb4b35570fc704dbb9a70c73… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh for galaxy tarballs Do not assume git is installed and the `.git` directory is present. Fix https://github.com/galaxyproject/galaxy/issues/5466 Commit: 3f50b45a4e3016a211dcbd0876bb95acb29cf900 https://github.com/galaxyproject/galaxy/commit/3f50b45a4e3016a211dcbd0876bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #5445 from gregvonkuster/add-ideaspre [18.01] Add support for the ideaspre datatype Commit: d91078024bf3e9404aaca1c8655a5bc2b451ebc8 https://github.com/galaxyproject/galaxy/commit/d91078024bf3e9404aaca1c8655a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone [18.01] Fix common_startup.sh for galaxy tarballs Commit: 10ff797ac77da470cf2078059b3235cee04570ff https://github.com/galaxyproject/galaxy/commit/10ff797ac77da470cf2078059b32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.01' into dev Conflicts: scripts/common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/0ca7afb343d8...10ff797ac77d

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[galaxyproject/infrastructure-playbook] db9646: Enable the monitor for influxdb
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: db9646bca42d6a61e3de2d89fe8d1dfdcea84014 https://github.com/galaxyproject/infrastructure-playbook/commit/db9646bca42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Enable the monitor for influxdb

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[galaxyproject/galaxy] b463be: Add nodeenv to dev requirements
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b463be78a5066c7e6c389c43af2bd863f05e4a80 https://github.com/galaxyproject/galaxy/commit/b463be78a5066c7e6c389c43af2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 977bbf1481b2fd36512f869c01f0af6ba4099a92 https://github.com/galaxyproject/galaxy/commit/977bbf1481b2fd36512f869c01f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: eba3fb4b35570fc704dbb9a70c733293a2ee4514 https://github.com/galaxyproject/galaxy/commit/eba3fb4b35570fc704dbb9a70c73… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh for galaxy tarballs Do not assume git is installed and the `.git` directory is present. Fix https://github.com/galaxyproject/galaxy/issues/5466 Commit: d91078024bf3e9404aaca1c8655a5bc2b451ebc8 https://github.com/galaxyproject/galaxy/commit/d91078024bf3e9404aaca1c8655a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone [18.01] Fix common_startup.sh for galaxy tarballs Compare: https://github.com/galaxyproject/galaxy/compare/3f50b45a4e30...d91078024bf3

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[galaxyproject/galaxy] b5945a: Add IdeasPre datatype subclassed from Rgenetics
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b5945ad3e3a972acb41c87c2ddeeff222779020c https://github.com/galaxyproject/galaxy/commit/b5945ad3e3a972acb41c87c2ddee… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Add IdeasPre datatype subclassed from Rgenetics Commit: 3fdd4edc5c1954dc750dfeff03cb3205ee1b6042 https://github.com/galaxyproject/galaxy/commit/3fdd4edc5c1954dc750dfeff03cb… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Subclass IdeasPre from Html Commit: 3f50b45a4e3016a211dcbd0876bb95acb29cf900 https://github.com/galaxyproject/galaxy/commit/3f50b45a4e3016a211dcbd0876bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #5445 from gregvonkuster/add-ideaspre [18.01] Add support for the ideaspre datatype Compare: https://github.com/galaxyproject/galaxy/compare/64e4e8b572b8...3f50b45a4e30

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[galaxyproject/infrastructure-playbook] 84730b: Update postgresql_objects role
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 84730b8a7f17d3d60dab304ffa7c2e23b4eed8a0 https://github.com/galaxyproject/infrastructure-playbook/commit/84730b8a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/natefoo.postgresql_objects/README.md M roles/natefoo.postgresql_objects/meta/.galaxy_install_info M roles/natefoo.postgresql_objects/tasks/main.yml Log Message: ----------- Update postgresql_objects role Commit: 7c023ee85662f5165e71a7eea8b7cd101c3ba3ea https://github.com/galaxyproject/infrastructure-playbook/commit/7c023ee8566… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/sentry/tasks/main.yml M roles/sentry/templates/sentry.conf.py.j2 M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M taccenv/group_vars/statsservers.yml Log Message: ----------- Email and other fixes for stats/sentry Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b27e8c6159…

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