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

[galaxyproject/usegalaxy-playbook] bfc167: Update SSL certs
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfc167bedf63a660d83427562f78960b6bd3963c https://github.com/galaxyproject/usegalaxy-playbook/commit/bfc167bedf63a660… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M common/secret_vars/ssl.yml M common_infrastructure.yml M files/ssl/athena.galaxyproject.org_cert.pem R files/ssl/montana.galaxyproject.org_cert.pem A files/ssl/radegast.galaxyproject.org_cert.pem R files/ssl/wildcard_cert.pem M templates/nginx/cloudlaunch.j2 Log Message: ----------- Update SSL certs Commit: 23c400852d03206eb49265dbb6ee0c2517a680c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/23c400852d03206e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/57ec60640226...…

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[galaxyproject/galaxy] ce418d: Resolve conflicting label CSS class.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce418d33fe221b27da162717a208381aa8042ea8 https://github.com/galaxyproject/galaxy/commit/ce418d33fe221b27da162717a208… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Resolve conflicting label CSS class. Commit: f1abf1e9ab4dc4f1d3e6987c6bb68ab3b188083c https://github.com/galaxyproject/galaxy/commit/f1abf1e9ab4dc4f1d3e6987c6bb6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1086 from jgoecks/trackster-pos-label Resolve conflicting label CSS class for trackster. Compare: https://github.com/galaxyproject/galaxy/compare/2dcb92aa0e83...f1abf1e9ab4d

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[galaxyproject/galaxy] ffda4a: Allow dockerized toolshed tests.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffda4aa2cd033e8953ef780fb553afbc77e4a7f4 https://github.com/galaxyproject/galaxy/commit/ffda4aa2cd033e8953ef780fb553… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Allow dockerized toolshed tests. Commit: 096adbf8d0776d4b1085705f2881c2d46ab06611 https://github.com/galaxyproject/galaxy/commit/096adbf8d0776d4b1085705f2881… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Collect apt installs in one place. Commit: 1766b896e30ed1b2bc5aa5341cf19d313628c4f4 https://github.com/galaxyproject/galaxy/commit/1766b896e30ed1b2bc5aa5341cf1… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M config/datatypes_conf.xml.sample M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh A scripts/api/library_upload_dir.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge -dev. Commit: 2dcb92aa0e83f9893595b68222fc62cf052a9220 https://github.com/galaxyproject/galaxy/commit/2dcb92aa0e83f9893595b68222fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Merge pull request #942 from davebx/docker Enable dockerized toolshed tests. Compare: https://github.com/galaxyproject/galaxy/compare/625d49e2de07...2dcb92aa0e83

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[galaxyproject/galaxy] d824cc: In interactive environments, the /import volume ca...
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/release_15.10 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 Compare: https://github.com/galaxyproject/galaxy/compare/a3034ab6d99d...64b084067c73

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[galaxyproject/usegalaxy-playbook] 2656d9: Test mutable configs
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2656d95c0c1fb47012ef82a6d1a60599c975a323 https://github.com/galaxyproject/usegalaxy-playbook/commit/2656d95c0c1fb470… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: 57ec60640226b51f7664812ab99de1d7a5d56324 https://github.com/galaxyproject/usegalaxy-playbook/commit/57ec60640226b51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- IPython config changes for Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5ad413739ce4...…

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[galaxyproject/usegalaxy-playbook] 5ad413: Run kraken in multi partition
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ad413739ce404f9efe3e3163844f0a881fd8908 https://github.com/galaxyproject/usegalaxy-playbook/commit/5ad413739ce404f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Run kraken in multi partition

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[galaxyproject/galaxy] d6d8e5: upload.py: Remove unused function parameter
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6d8e5ef86bbfe460709c82590596252de2d5a71 https://github.com/galaxyproject/galaxy/commit/d6d8e5ef86bbfe460709c8259059… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- upload.py: Remove unused function parameter Commit: 625d49e2de074c240555efbff1319c6ddf9676a1 https://github.com/galaxyproject/galaxy/commit/625d49e2de074c240555efbff131… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #1078 from einon/einon upload.py: Remove unused function parameter Compare: https://github.com/galaxyproject/galaxy/compare/2214f887a668...625d49e2de07

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[galaxyproject/galaxy] 240da5: Update both lped pbed pbed lped converters to be i...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 240da5e720c069b08caf77828dc4e3e598b56089 https://github.com/galaxyproject/galaxy/commit/240da5e720c069b08caf77828dc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Update both lped pbed pbed lped converters to be in sync with their html. Thanks @nsoranzo. Commit: 2214f887a668a4eed1e3b94d880c57e2e57ef9a1 https://github.com/galaxyproject/galaxy/commit/2214f887a668a4eed1e3b94d880c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Merge pull request #1072 from dannon/fix_lped_report_output Update both lped pbed pbed lped converters to be in sync with their h… Compare: https://github.com/galaxyproject/galaxy/compare/3a70dc395a2a...2214f887a668

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[galaxyproject/galaxy] 30668f: Fix for reloading tools that have non-standard too...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30668fe5344192e7b17f05060062fa330c5496a0 https://github.com/galaxyproject/galaxy/commit/30668fe5344192e7b17f05060062… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Fix for reloading tools that have non-standard tool_ids/versions. Commit: 3f898677f19d7600648802b1a428ce916dd35e11 https://github.com/galaxyproject/galaxy/commit/3f898677f19d7600648802b1a428… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- HTML escape tool name, id, version, on tool reload message. Commit: 045832bd8ecd4515d134cb5e05f64d2b7b4e933a https://github.com/galaxyproject/galaxy/commit/045832bd8ecd4515d134cb5e05f6… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Also escape tool name, id, version in message when removing tools. Commit: 3a70dc395a2afb73363440edaa624d6f053467d2 https://github.com/galaxyproject/galaxy/commit/3a70dc395a2afb73363440edaa62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Merge pull request #1050 from blankenberg/reload-tool-id-fix Fix for reloading tools that have non-standard tool_ids/versions. Compare: https://github.com/galaxyproject/galaxy/compare/926b1a2cdd3c...3a70dc395a2a

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[galaxyproject/galaxy] 67d0bc: Trivial: Replace unnecessary duplicated var check ...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67d0bcb5b3bba9c13bfa0c556a4460e1304b63a9 https://github.com/galaxyproject/galaxy/commit/67d0bcb5b3bba9c13bfa0c556a44… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Trivial: Replace unnecessary duplicated var check with 'else if' Commit: 926b1a2cdd3c772f214a2ae62945427d2c36402f https://github.com/galaxyproject/galaxy/commit/926b1a2cdd3c772f214a2ae62945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Merge pull request #1073 from einon/einon Trivial: Replace unnecessary duplicated var check with 'else if' Compare: https://github.com/galaxyproject/galaxy/compare/1cf5af4c2023...926b1a2cdd3c

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