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

[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/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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