August 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 66f069: Install Java on Jenkins hosts
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 66f069f552c8cdb5465493e698280dba19be8b65 https://github.com/galaxyproject/infrastructure-playbook/commit/66f069f552c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M galaxyenv/group_vars/jenkinsservers.yml A galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Install Java on Jenkins hosts

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[galaxyproject/galaxy] 6516f2: Update common_startup.sh to require python2.7 in ....
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6516f20602259a7b55da57ed6c668b2590a7645c https://github.com/galaxyproject/galaxy/commit/6516f20602259a7b55da57ed6c66… Author: Ben <BenjaminHCCarr(a)users.noreply.github.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Update common_startup.sh to require python2.7 in .venv by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need. The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python % mkdir ~/galaxy-python % ln -s /path/to/python2.7 ~/galaxy-python/python % export PATH=~/galaxy-python:$PATH Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want. This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible. This edit built fine on OS X 10.10.5 python installed: 2.6, 2.7, 3.2, 3.5 galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main Starting server in PID 69210. serving on http://127.0.0.1:8080 /Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) 127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36" Commit: 77b7e65d2b12b3e8de73056fa08d10f874330ae6 https://github.com/galaxyproject/galaxy/commit/77b7e65d2b12b3e8de73056fa08d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2756 from BenjaminHCCarr/patch-2 Update common_startup.sh to require python2.7 in .venv Commit: 8c1be9123151db83f74096ac2ce56681df82f36c https://github.com/galaxyproject/galaxy/commit/8c1be9123151db83f74096ac2ce5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/580ace125aab...8c1be9123151

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[galaxyproject/galaxy] 6516f2: Update common_startup.sh to require python2.7 in ....
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6516f20602259a7b55da57ed6c668b2590a7645c https://github.com/galaxyproject/galaxy/commit/6516f20602259a7b55da57ed6c66… Author: Ben <BenjaminHCCarr(a)users.noreply.github.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Update common_startup.sh to require python2.7 in .venv by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need. The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python % mkdir ~/galaxy-python % ln -s /path/to/python2.7 ~/galaxy-python/python % export PATH=~/galaxy-python:$PATH Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want. This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible. This edit built fine on OS X 10.10.5 python installed: 2.6, 2.7, 3.2, 3.5 galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main Starting server in PID 69210. serving on http://127.0.0.1:8080 /Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) 127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36" Commit: 77b7e65d2b12b3e8de73056fa08d10f874330ae6 https://github.com/galaxyproject/galaxy/commit/77b7e65d2b12b3e8de73056fa08d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2756 from BenjaminHCCarr/patch-2 Update common_startup.sh to require python2.7 in .venv Compare: https://github.com/galaxyproject/galaxy/compare/a334b189ba32...77b7e65d2b12

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[galaxyproject/galaxy] 34f9a6: disable hg middleware
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34f9a6b5c26a0d8b0d61e48cd34bc072c82e1e0d https://github.com/galaxyproject/galaxy/commit/34f9a6b5c26a0d8b0d61e48cd34b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- disable hg middleware Commit: af4fab16f58c36ea66328725e5bdcfaa3acbacda https://github.com/galaxyproject/galaxy/commit/af4fab16f58c36ea66328725e5bd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- remove unwanted hg middleware remove obsolete test Commit: b10e1cbb971786d86f4d79de0e04d4d3f1f9f7c1 https://github.com/galaxyproject/galaxy/commit/b10e1cbb971786d86f4d79de0e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- remove obsolete config option Commit: 9618386fd0b7511aead50b14dea763b32bfdd4a8 https://github.com/galaxyproject/galaxy/commit/9618386fd0b7511aead50b14dea7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- remove code related to hg push Commit: 580ace125aaba415582a5ca28392674d7ab9cedf https://github.com/galaxyproject/galaxy/commit/580ace125aaba415582a5ca28392… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- Merge pull request #2753 from martenson/disable_hg_middleware remove TS hg middleware Compare: https://github.com/galaxyproject/galaxy/compare/0e9c04425671...580ace125aab

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[galaxyproject/galaxy] 5c79aa: Allow link buttons to trigger regular click events
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c79aa8fbc727feec6fa2041881645acdaed75f4 https://github.com/galaxyproject/galaxy/commit/5c79aa8fbc727feec6fa20418816… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Allow link buttons to trigger regular click events Commit: 83d4ebd0348cae7c9d0056e37b269c96768d0312 https://github.com/galaxyproject/galaxy/commit/83d4ebd0348cae7c9d0056e37b26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Fix unused href parameter when adding scratchbook frames Commit: 258e4a7b669edb2aca15e295353db384bc72575a https://github.com/galaxyproject/galaxy/commit/258e4a7b669edb2aca15e295353d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Merge pull request #2744 from guerler/fix_scratchbook_href [16.07] Fix unused href parameter when adding scratchbook frames Commit: fe3db95eec8fd942a9a46ad05c579c41eda9705e https://github.com/galaxyproject/galaxy/commit/fe3db95eec8fd942a9a46ad05c57… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Merge branch 'release_16.07' into fix_history_refresh Commit: 8c57ed7e5432e4f92b95bc41fc657b562db18430 https://github.com/galaxyproject/galaxy/commit/8c57ed7e5432e4f92b95bc41fc65… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #2743 from guerler/fix_history_refresh [16.07] Allow link buttons to trigger regular click events Commit: 786da21a3bd97da1c2f349f77515fed2b3713d6c https://github.com/galaxyproject/galaxy/commit/786da21a3bd97da1c2f349f77515… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Hide form instead of removing it to preserve attached listento events Commit: b39f2143fac4f2be29477d4b1c5542bfe7dd0946 https://github.com/galaxyproject/galaxy/commit/b39f2143fac4f2be29477d4b1c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. Commit: 3f8f9b7bbb0c565a07de43820dcfa5ed6e4d03e1 https://github.com/galaxyproject/galaxy/commit/3f8f9b7bbb0c565a07de43820dcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #2737 from guerler/hide_form_on_success [16.07] Hide form instead of removing it to preserve attached listenTo events Commit: 64a55728d6056930aa8532262549f4ed657e4086 https://github.com/galaxyproject/galaxy/commit/64a55728d6056930aa8532262549… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix docker command_list command_list always generates ***docker docker*** Without fix , docker runs new image which doesn't exist , docker fetch it in ***docker run*** command and it generates progress information to stderr. It will end galaxy job as fail. But rerun same job, it will be success , because of the image is already exists , fetch process never happens. Commit: 7d5bbf7a44212cd5ec9cb07359fa1f49146b50f2 https://github.com/galaxyproject/galaxy/commit/7d5bbf7a44212cd5ec9cb07359fa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #2749 from jmchilton/backport_2748 [16.07] Backport #2748 Commit: a7664f00f92a97258050d580aef1b6e439cc2f6d https://github.com/galaxyproject/galaxy/commit/a7664f00f92a97258050d580aef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. Commit: a334b189ba325a806da26cc7ac005c55960e966c https://github.com/galaxyproject/galaxy/commit/a334b189ba325a806da26cc7ac00… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 0e9c044256717bea6f46651be7c3660a377be8e2 https://github.com/galaxyproject/galaxy/commit/0e9c044256717bea6f46651be7c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M static/maps/layout/scratchbook.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d6ce0161388e...0e9c04425671

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[galaxyproject/galaxy] b39f21: Fix to mount job directory in Docker for #1688.
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: b39f2143fac4f2be29477d4b1c5542bfe7dd0946 https://github.com/galaxyproject/galaxy/commit/b39f2143fac4f2be29477d4b1c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. Commit: a7664f00f92a97258050d580aef1b6e439cc2f6d https://github.com/galaxyproject/galaxy/commit/a7664f00f92a97258050d580aef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. Commit: a334b189ba325a806da26cc7ac005c55960e966c https://github.com/galaxyproject/galaxy/commit/a334b189ba325a806da26cc7ac00… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/7d5bbf7a4421...a334b189ba32

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[galaxyproject/galaxy] 92948b: Overload select wrapper`s concat function
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Overload select wrapper`s concat function Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1 https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. Commit: e37850386ecc8122abeb6695ffc76eb513f34516 https://github.com/galaxyproject/galaxy/commit/e37850386ecc8122abeb6695ffc7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 6b64af72deafee0382cb5b9c83ed39a3fa42e1c9 https://github.com/galaxyproject/galaxy/commit/6b64af72deafee0382cb5b9c83ed… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Conflicts: client/galaxy/scripts/mvc/history/history-contents.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 654748763af10aa87d3afe9fdf9ea686520ede7e https://github.com/galaxyproject/galaxy/commit/654748763af10aa87d3afe9fdf9e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: d550024d56c063bb78e4855395cfbf0cc440fe08 https://github.com/galaxyproject/galaxy/commit/d550024d56c063bb78e4855395cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js static/scripts/bundled/login.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: 0d49b06bac4a5c4a4b94e48517d1c0f5de713d42 https://github.com/galaxyproject/galaxy/commit/0d49b06bac4a5c4a4b94e48517d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- repack Commit: 132bd4dd57e084ec8e743e1360e7d2a0faa29ac6 https://github.com/galaxyproject/galaxy/commit/132bd4dd57e084ec8e743e1360e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge branch 'backport_2613' into release_16.04 (and rebuild client) Commit: 68a64182c14af9f4cc10915c466177292d24ebfc https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c4661… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428 https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Commit: b39f2143fac4f2be29477d4b1c5542bfe7dd0946 https://github.com/galaxyproject/galaxy/commit/b39f2143fac4f2be29477d4b1c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. Commit: a7664f00f92a97258050d580aef1b6e439cc2f6d https://github.com/galaxyproject/galaxy/commit/a7664f00f92a97258050d580aef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. Commit: fb76aa0a938a2498d3206e6039bc1d9906e6c2ce https://github.com/galaxyproject/galaxy/commit/fb76aa0a938a2498d3206e6039bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M test/base/driver_util.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/a5b836e9eeea...fb76aa0a938a

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[galaxyproject/galaxy] b39f21: Fix to mount job directory in Docker for #1688.
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: b39f2143fac4f2be29477d4b1c5542bfe7dd0946 https://github.com/galaxyproject/galaxy/commit/b39f2143fac4f2be29477d4b1c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. Commit: a7664f00f92a97258050d580aef1b6e439cc2f6d https://github.com/galaxyproject/galaxy/commit/a7664f00f92a97258050d580aef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. Compare: https://github.com/galaxyproject/galaxy/compare/e4ca3bf80fca...a7664f00f92a

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[galaxyproject/galaxy] 64a557: Fix docker command_list
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 64a55728d6056930aa8532262549f4ed657e4086 https://github.com/galaxyproject/galaxy/commit/64a55728d6056930aa8532262549… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix docker command_list command_list always generates ***docker docker*** Without fix , docker runs new image which doesn't exist , docker fetch it in ***docker run*** command and it generates progress information to stderr. It will end galaxy job as fail. But rerun same job, it will be success , because of the image is already exists , fetch process never happens. Commit: 7d5bbf7a44212cd5ec9cb07359fa1f49146b50f2 https://github.com/galaxyproject/galaxy/commit/7d5bbf7a44212cd5ec9cb07359fa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #2749 from jmchilton/backport_2748 [16.07] Backport #2748 Compare: https://github.com/galaxyproject/galaxy/compare/3f8f9b7bbb0c...7d5bbf7a4421

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[galaxyproject/galaxy] 35361d: Fix docker command_list
by GitHub 08 Aug '16

08 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35361d1259c3492e2721e93edc713dd9dfea7eb3 https://github.com/galaxyproject/galaxy/commit/35361d1259c3492e2721e93edc71… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix docker command_list command_list always generates ***docker docker*** Without fix , docker runs new image which doesn't exist , docker fetch it in ***docker run*** command and it generates progress information to stderr. It will end galaxy job as fail. But rerun same job, it will be success , because of the image is already exists , fetch process never happens. Commit: d6ce0161388ecf30ad23ecb17090f2b2eea5f296 https://github.com/galaxyproject/galaxy/commit/d6ce0161388ecf30ad23ecb17090… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #2748 from manabuishii/patch-2 Fix docker command_list Compare: https://github.com/galaxyproject/galaxy/compare/5b905fece8d3...d6ce0161388e

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