November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 937f99: Fix API installation of tool_dependencies
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 937f99b851e2078152c851a0b552c00b99167747 https://github.com/galaxyproject/galaxy/commit/937f99b851e2078152c851a0b552… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 3ffa607c15a70a532a7d21a0b3b1a46171e53171 https://github.com/galaxyproject/galaxy/commit/3ffa607c15a70a532a7d21a0b3b1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Deprecate old library UI in the "Shared Data" menu. Commit: e61e30cde549c448375b555aadfc85b235b4871a https://github.com/galaxyproject/galaxy/commit/e61e30cde549c448375b555aadfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1100 from martenson/fix-ts-api-install [15.10] Fix API installation of tool_dependencies Commit: 05e66827d40151c0cd1729299fa82a510138359e https://github.com/galaxyproject/galaxy/commit/05e66827d40151c0cd1729299fa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge pull request #1112 from nsoranzo/release_15.10_data_libraries_beta [15.10] Deprecate old library UI in the "Shared Data" menu. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: c252987b4c5febb7fa10db3c7359449f325fc9ca https://github.com/galaxyproject/galaxy/commit/c252987b4c5febb7fa10db3c7359… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3d933edd32dd...c252987b4c5f

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[galaxyproject/galaxy] d824cc: In interactive environments, the /import volume ca...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d824cca31fcebe97b8c7cfd1040eecbb9e5f03d3 https://github.com/galaxyproject/galaxy/commit/d824cca31fcebe97b8c7cfd1040e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- In interactive environments, the /import volume can now be made conditional. Also, fix a bug when using a proxy for the node proxy and cookie_path is / Commit: c4351413265796dacc15b8e3fc7382b8514f5b59 https://github.com/galaxyproject/galaxy/commit/c4351413265796dacc15b8e3fc73… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Built image tag differs from intended. Commit: 64b084067c73cea1de455e4816d73101c3752165 https://github.com/galaxyproject/galaxy/commit/64b084067c73cea1de455e4816d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1076 from natefoo/ie-conditional-import-volume [15.10] Fix a bug in IEs when proxying the proxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad25923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Commit: 937f99b851e2078152c851a0b552c00b99167747 https://github.com/galaxyproject/galaxy/commit/937f99b851e2078152c851a0b552… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 3ffa607c15a70a532a7d21a0b3b1a46171e53171 https://github.com/galaxyproject/galaxy/commit/3ffa607c15a70a532a7d21a0b3b1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Deprecate old library UI in the "Shared Data" menu. Commit: e61e30cde549c448375b555aadfc85b235b4871a https://github.com/galaxyproject/galaxy/commit/e61e30cde549c448375b555aadfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1100 from martenson/fix-ts-api-install [15.10] Fix API installation of tool_dependencies Commit: 05e66827d40151c0cd1729299fa82a510138359e https://github.com/galaxyproject/galaxy/commit/05e66827d40151c0cd1729299fa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge pull request #1112 from nsoranzo/release_15.10_data_libraries_beta [15.10] Deprecate old library UI in the "Shared Data" menu. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Compare: https://github.com/galaxyproject/galaxy/compare/a3034ab6d99d...73f46f4e0814

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[galaxyproject/galaxy] 040118: Encode unicode string before passing to hashlib.sh...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Compare: https://github.com/galaxyproject/galaxy/compare/05e66827d401...73f46f4e0814

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[galaxyproject/galaxy] f2356e: extend API interactor to allow http PATCH and DELE...
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f2356ef819111fe2507cc96059f5e1da7fbf6b3e https://github.com/galaxyproject/galaxy/commit/f2356ef819111fe2507cc96059f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/base/api.py M test/base/interactor.py Log Message: ----------- extend API interactor to allow http PATCH and DELETE testing Commit: 43dc7a52e5289acdb681c30a2aeb49bb2f68e61d https://github.com/galaxyproject/galaxy/commit/43dc7a52e5289acdb681c30a2aeb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/api/test_libraries.py M test/base/interactor.py Log Message: ----------- add more API tests for data libraries Commit: 3d933edd32dd872a1e660a061cdef4cffc587ec0 https://github.com/galaxyproject/galaxy/commit/3d933edd32dd872a1e660a061cde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M test/api/test_libraries.py M test/base/api.py M test/base/interactor.py Log Message: ----------- Merge pull request #1074 from martenson/lib-api-tests [WIP] add more data libraries API tests Compare: https://github.com/galaxyproject/galaxy/compare/729ed463aa87...3d933edd32dd

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[galaxyproject/infrastructure-playbook] bcb7d6: Manage services in Galaxy env
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bcb7d6375433c712807eb867e947ab6f8c23cefa https://github.com/galaxyproject/infrastructure-playbook/commit/bcb7d637543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M galaxyenv/playbook.yml Log Message: ----------- Manage services in Galaxy env

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[galaxyproject/infrastructure-playbook] 4ab883: Disable the docker daemon on Galaxy servers
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4ab8830e9577e3ca550c0e496c2d879239e3b811 https://github.com/galaxyproject/infrastructure-playbook/commit/4ab8830e957… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M common_roles M taccenv/group_vars/galaxyservers.yml M taccenv/playbook.yml Log Message: ----------- Disable the docker daemon on Galaxy servers

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[galaxyproject/infrastructure-playbook] dee7ba: Install docker on Galaxy servers
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dee7bab26a651da3f316bb6ea972bcd378932314 https://github.com/galaxyproject/infrastructure-playbook/commit/dee7bab26a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M common_roles M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Install docker on Galaxy servers

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[galaxyproject/galaxy] d40d38: CRAM format
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d40d384a8672b5bc58db210a6e1aca41cb50e9d6 https://github.com/galaxyproject/galaxy/commit/d40d384a8672b5bc58db210a6e1a… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- CRAM format Commit: 3df95ae9a6f081090bb554b0778f145f0ec622fa https://github.com/galaxyproject/galaxy/commit/3df95ae9a6f081090bb554b0778f… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- flake8 Commit: 729ed463aa87d07bc27dc669ba80d0187dd85b47 https://github.com/galaxyproject/galaxy/commit/729ed463aa87d07bc27dc669ba80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1108 from yhoogstrate/cram_datatype CRAM datatype definiton Compare: https://github.com/galaxyproject/galaxy/compare/f4db7587565c...729ed463aa87

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[galaxyproject/galaxy] ee721c: Check len files during download from UCSC.
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee721c5d360e774636d271db673d1485ddcc7a21 https://github.com/galaxyproject/galaxy/commit/ee721c5d360e774636d271db673d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M cron/build_chrom_db.py Log Message: ----------- Check len files during download from UCSC. Do not create file in case of errors, so the cron script will not overwrite a good file with a bad one. Commit: f4db7587565c912005da35410228b293b11555cd https://github.com/galaxyproject/galaxy/commit/f4db7587565c912005da35410228… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M cron/build_chrom_db.py Log Message: ----------- Merge pull request #1066 from nsoranzo/cron_ucsc Check len files during download from UCSC. Compare: https://github.com/galaxyproject/galaxy/compare/1063c175be53...f4db7587565c

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[galaxyproject/infrastructure-playbook] 611c8b: Minor restructuring and add a couple TACC hosts fo...
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 611c8be1579632adec55900235f0266c12654ad8 https://github.com/galaxyproject/infrastructure-playbook/commit/611c8be1579… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M ansible.cfg A galaxyenv/playbook.yml R playbook.yml A taccenv/group_vars/galaxyservers.yml A taccenv/inventory A taccenv/playbook.yml Log Message: ----------- Minor restructuring and add a couple TACC hosts for use of the packages role

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