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

[galaxyproject/galaxy] 785f81: Add developer documentation to docs
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 785f81989627db26b3799b0e6d5123213fcec9e4 https://github.com/galaxyproject/galaxy/commit/785f81989627db26b3799b0e6d51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst Log Message: ----------- Add developer documentation to docs Commit: 86c3175fcda4ff85505ecfcd78cf2b302909a7a7 https://github.com/galaxyproject/galaxy/commit/86c3175fcda4ff85505ecfcd78cf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/_api_quickstart.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/ts_api_doc.rst Log Message: ----------- Extract quickstart, reorg GX/TS Doc index Commit: 0bfa99725463f1807816e5c0bdeacf46eb186c55 https://github.com/galaxyproject/galaxy/commit/0bfa99725463f1807816e5c0bdea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: R doc/source/_api_quickstart.rst Log Message: ----------- Remove unused file Commit: b6105acd2b7f0957c315a63bcf083a596189383b https://github.com/galaxyproject/galaxy/commit/b6105acd2b7f0957c315a63bcf08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- merge... Commit: f7a68ec29567a4dc3067ab0b3bccdc6c32c975d3 https://github.com/galaxyproject/galaxy/commit/f7a68ec29567a4dc3067ab0b3bcc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/workflow/run.py M scripts/common_startup.sh M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map A static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js A static/scripts/mvc/upload/upload-row.js A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 2166f876bc938e9837bbb974e24a670e1e12fe98 https://github.com/galaxyproject/galaxy/commit/2166f876bc938e9837bbb974e24a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg M doc/source/index.rst Log Message: ----------- First draft of GIE admin docs Commit: 79c75e6e21aa894c949540160d87f1b7a6c43b39 https://github.com/galaxyproject/galaxy/commit/79c75e6e21aa894c949540160d87… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Added docker-on-another-host Commit: 94c61f9f7f31189f3d7d265cf94fab198f5007b8 https://github.com/galaxyproject/galaxy/commit/94c61f9f7f31189f3d7d265cf94f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Add long tutorial on how-to-GIE Commit: 4b8f9b22a54f828075a7b574762ef0fc19e500dd https://github.com/galaxyproject/galaxy/commit/4b8f9b22a54f828075a7b574762e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct highlighting, and small bugs/typos Commit: 6db64967197b0ee7dff6c4df31d6281c89294720 https://github.com/galaxyproject/galaxy/commit/6db64967197b0ee7dff6c4df31d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct docker_port/proxy_prefix Commit: ed0fefaa4339d8ec96e60c98befa3fa2e5ff07b4 https://github.com/galaxyproject/galaxy/commit/ed0fefaa4339d8ec96e60c98befa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Full list of env vars, more doc corrections Commit: 928345fad7aa16bd1c32133e9b571954faddd0f3 https://github.com/galaxyproject/galaxy/commit/928345fad7aa16bd1c32133e9b57… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fixed the image to show up The .* did not do the trick, added the .png extension so we could see the image. There is still the "interactive_environments_success.png" missing though! If you want me to take the picture, I can. Just need to know exactly what you want to show :p Commit: 98601084ec7f130f0b7dd27354648afd24cb1e78 https://github.com/galaxyproject/galaxy/commit/98601084ec7f130f0b7dd2735464… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #11 from remimarenco/patch-1 Fixed the interactive_environments' image to show up Commit: 771376a742fc1a248cc2223acebb27f5fd24ba43 https://github.com/galaxyproject/galaxy/commit/771376a742fc1a248cc2223acebb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: A doc/source/admin/interactive_environments_success.png Log Message: ----------- Added success picture Commit: e81517bb9cefb7e4ddab991d3da59ae63619fd81 https://github.com/galaxyproject/galaxy/commit/e81517bb9cefb7e4ddab991d3da5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge branch 'gie-docs' of github.com:erasche/galaxy into gie-docs Commit: de03710756c1858b47802bae5b3d3d67fde248b7 https://github.com/galaxyproject/galaxy/commit/de03710756c1858b47802bae5b3d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Comment out default value Commit: 76db6d5274f7fd527d7e161b4ec21492176096f7 https://github.com/galaxyproject/galaxy/commit/76db6d5274f7fd527d7e161b4ec2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Link to the wiki Commit: 86aa3ca22bb820e240642aca64131ff7a5350bd2 https://github.com/galaxyproject/galaxy/commit/86aa3ca22bb820e240642aca6413… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst M doc/source/index.rst Log Message: ----------- Document that this isn't the primary admin docs Commit: d8ce3c25df0e6f0e44278e2dadd771d2030ae087 https://github.com/galaxyproject/galaxy/commit/d8ce3c25df0e6f0e44278e2dadd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg A doc/source/admin/interactive_environments_success.png M doc/source/dev/faq.rst M doc/source/index.rst Log Message: ----------- Merge pull request #803 from erasche/gie-docs Document GIEs Compare: https://github.com/galaxyproject/galaxy/compare/c7c269572e61...d8ce3c25df0e

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[galaxyproject/galaxy] 2c45f3: UI, Collections: correct foldout expansion for col...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c45f356a942a64fb6506358d793bc2c4b4579f9 https://github.com/galaxyproject/galaxy/commit/2c45f356a942a64fb6506358d793… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- UI, Collections: correct foldout expansion for collections only re-rendering on 'populated' or 'visible' change; correct foldout expansion in published histories by giving dataset collection elements an api endpoint and moving 'rerunnable' and 'creating_job' fetch into li-edit Commit: c7c269572e618710b87986b3f4b51d187140dd7e https://github.com/galaxyproject/galaxy/commit/c7c269572e618710b87986b3f4b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #819 from carlfeberhard/fix.collection-expansion UI, Collections: correct foldout expansion for collections only re-re… Compare: https://github.com/galaxyproject/galaxy/compare/6ee9a08cf2d3...c7c269572e61

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[galaxyproject/usegalaxy-playbook] e7212a: Test mutable configs
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e7212ad3e22a5d8c50aacec8f06b47294f15f99d https://github.com/galaxyproject/usegalaxy-playbook/commit/e7212ad3e22a5d8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.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: b4eda1dd56b85084bd43be94df224539bc472575 https://github.com/galaxyproject/usegalaxy-playbook/commit/b4eda1dd56b85084… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M production/group_vars/all.yml M production/group_vars/pulsarservers.yml Log Message: ----------- Update Main Galaxy and Pulsar Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/96d7eadf57b0...…

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[galaxyproject/infrastructure-playbook] bad344: Don't attempt delivery from EC2 via IPv6 since EC2...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bad3440527eb3dd571d6ad028a5e09c2fb1e6753 https://github.com/galaxyproject/infrastructure-playbook/commit/bad3440527e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M roles/postfix/templates/main.cf.j2 Log Message: ----------- Don't attempt delivery from EC2 via IPv6 since EC2 still doesn't really do IPv6 in a useful way. =(

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[galaxyproject/infrastructure-playbook] 1fafed: Move some athena things over from usegalaxy-playbo...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1fafed283871b4eaf83747c445af7bbcdc140979 https://github.com/galaxyproject/infrastructure-playbook/commit/1fafed28387… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A galaxyenv/group_vars/ec2hosts.yml A galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/athena.galaxyproject.org.yml M roles/postfix/templates/main.cf.j2 Log Message: ----------- Move some athena things over from usegalaxy-playbook. Allow mail relaying through chouffe in the EC2 VPC.

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[galaxyproject/usegalaxy-playbook] 70595d: Moved some athena stuff to infrastructure-playbook
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70595dbfc1533f3707eca4cc04d9840d308d69af https://github.com/galaxyproject/usegalaxy-playbook/commit/70595dbfc1533f37… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M common/host_vars/athena.galaxyproject.org.yml Log Message: ----------- Moved some athena stuff to infrastructure-playbook Commit: 96d7eadf57b018a016cce4e0932964217510a215 https://github.com/galaxyproject/usegalaxy-playbook/commit/96d7eadf57b018a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .gitmodules M README.md M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py A files/galaxy/common/static/welcome_img/GCC2016TrNom.png A files/galaxy/common/static/welcome_img/Riboseq.png A files/galaxy/common/static/welcome_img/WhaleSharkGalaxy.png M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M files/galaxy/test.galaxyproject.org/config/tool_conf.xml R files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py A files/galaxy/test.galaxyproject.org/dynamic_rules/greenfield_select.py R files/galaxy/test.galaxyproject.org/nagios/echo_test_blacklight.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_greenfield.xml A files/galaxy/test.galaxyproject.org/tool_list.yaml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.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 A files/galaxy/usegalaxy.org/tool_list.yaml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M galaxy.yml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/group_vars/pulsarservers.yml M production/group_vars/toolshedservers.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml A production/secret_host_vars/default.yml A production/secret_host_vars/login5.stampede.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml R production/secret_vars/pulsarservers.yml M pulsar.yml M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml A roles/galaxyprojectdotorg.pulsar/templates/app.yml.j2 M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 A roles/galaxyprojectdotorg.tools/LICENSE A roles/galaxyprojectdotorg.tools/README.md A roles/galaxyprojectdotorg.tools/defaults/main.yml A roles/galaxyprojectdotorg.tools/files/README.md A roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample A roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py A roles/galaxyprojectdotorg.tools/files/tool_list.yaml A roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample A roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info A roles/galaxyprojectdotorg.tools/meta/main.yml A roles/galaxyprojectdotorg.tools/tasks/main.yml A roles/galaxyprojectdotorg.tools/tasks/tools.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml M stage/group_vars/toolshedservers.yml A stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml R stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml M stage/inventory A stage/secret_host_vars/default.yml A stage/secret_host_vars/greenfield.psc.xsede.org.yml A stage/secret_host_vars/login5.stampede.tacc.utexas.edu.yml M stage/secret_vars/galaxyservers.yml R stage/secret_vars/pulsarservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 A tools.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/85d58d667cd5...…

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[galaxyproject/infrastructure-playbook] 0ae54c: Update ssh key
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ae54c6d19e0667c51e519aafd4fd6b18707d69e https://github.com/galaxyproject/infrastructure-playbook/commit/0ae54c6d19e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Update ssh key Commit: 3f481bca5fd7b351253324f21fe9581320aafdfb https://github.com/galaxyproject/infrastructure-playbook/commit/3f481bca5fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M galaxyenv/host_vars/n2.galaxyproject.org.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/be07399e8d…

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[galaxyproject/galaxy] 57f023: Remove tool form mako
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f023529aef13723cb1555dc3ad5ea59aef009c https://github.com/galaxyproject/galaxy/commit/57f023529aef13723cb1555dc3ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Remove tool form mako Fix new-line Commit: f5a6e25ebd9d96a709781291cf04bc9e461216c6 https://github.com/galaxyproject/galaxy/commit/f5a6e25ebd9d96a709781291cf04… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Reinsert data_source tool execution into tool runner controller (requires separate PR) Commit: c1faf48d819ded4317995fe5f5ca436f847a4d09 https://github.com/galaxyproject/galaxy/commit/c1faf48d819ded4317995fe5f5ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add large message style and use for initial tool loading notifications Commit: 7777ea8f91928a9dd2c581eed53ba7e2ed1f3255 https://github.com/galaxyproject/galaxy/commit/7777ea8f91928a9dd2c581eed53b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Extend large ui-messages to cover states (info, warning, danger, success) Commit: 6d00f38f0a08281d5597872616154af0b3d306c2 https://github.com/galaxyproject/galaxy/commit/6d00f38f0a08281d559787261615… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M lib/pulsar/client/amqp_exchange.py M scripts/common_startup.sh M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js A test-data/1.RData M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 Conflicts: client/galaxy/scripts/mvc/tools/tools-form.js static/maps/mvc/tools/tools-form.js.map static/scripts/mvc/tools/tools-form.js Commit: 082c8952e03d11a44bd0cd354a3560f2471305e0 https://github.com/galaxyproject/galaxy/commit/082c8952e03d11a44bd0cd354a35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Undo initial errors Commit: 728c5450906c8b2ba395f06fa4dbe7e7cc5a7aa6 https://github.com/galaxyproject/galaxy/commit/728c5450906c8b2ba395f06fa4db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/tools.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools.js Log Message: ----------- Hide regular tool form for upload tool Commit: 6ee9a08cf2d3624985ceed2cf4f4bfd46ca24563 https://github.com/galaxyproject/galaxy/commit/6ee9a08cf2d3624985ceed2cf4f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-misc.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #786 from guerler/tool_form_003 Remove tool form mako, reduce tool runner, fix job resubmission options Compare: https://github.com/galaxyproject/galaxy/compare/b1a8aebad680...6ee9a08cf2d3

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[galaxyproject/galaxy] 1a13ef: API, Datasets: fix returned tuple from creating_jo...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a13efe488037aa30a98c80fdab8287bfdaaf923 https://github.com/galaxyproject/galaxy/commit/1a13efe488037aa30a98c80fdab8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- API, Datasets: fix returned tuple from creating_job; normalize id encoding, parens, naming; move both rerunnable and creating_job into datasets.py to allow (future?) use by lddas and ldas Commit: b1a8aebad680654bb2c9f19fe4b126e7fb3def2f https://github.com/galaxyproject/galaxy/commit/b1a8aebad680654bb2c9f19fe4b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #817 from carlfeberhard/fix.creating_job API, Datasets: fix returned tuple from creating_job Compare: https://github.com/galaxyproject/galaxy/compare/9aee2122251c...b1a8aebad680

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[galaxyproject/galaxy] 8a30d3: Fix change_password (destination for password rese...
by GitHub 29 Sep '15

29 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 8a30d3add42904f1117599790d63dfa273374d51 https://github.com/galaxyproject/galaxy/commit/8a30d3add42904f1117599790d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix change_password (destination for password reset link) to work w/ require_login Commit: 76fcde3274688db10eb259cdf25dbcc0d5187262 https://github.com/galaxyproject/galaxy/commit/76fcde3274688db10eb259cdf25d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #811 from dannon/prt_fix [15.07] Fix change_password (destination for password reset link) to work w/ … Compare: https://github.com/galaxyproject/galaxy/compare/8c9e8686a159...76fcde327468

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