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

[galaxyproject/galaxy] 8b121a: Improve logging message in output_collect.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b121ae31ca94c1c2a2c59b7f77da9c8097d2fa0 https://github.com/galaxyproject/galaxy/commit/8b121ae31ca94c1c2a2c59b7f77d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Improve logging message in output_collect. Conflicts: lib/galaxy/tools/parameters/output_collect.py Commit: 7c31a792fcdda60128848a53e9f567a99edb5c4a https://github.com/galaxyproject/galaxy/commit/7c31a792fcdda60128848a53e9f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow add_datasets to use optimized even if quota is used... Commit: ac14ad0897d4abb7875ad16a49dda7b6a43e3c84 https://github.com/galaxyproject/galaxy/commit/ac14ad0897d4abb7875ad16a49dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Optimization for discovering datasets for dynamic output collection. Batch up job creation and adding datasets to the history in order to eliminate a bunch of database flushes. Using the create_input_collection tool from PR #1958 to create an output collection with 100 elements - the optimization reduces the job finish time from 45 seconds to 15 seconds. Before: ``` galaxy.jobs DEBUG 2016-03-21 01:51:01,377 job 24 ended (finish() executed in (15474.472 ms)) ``` After: ``` galaxy.jobs DEBUG 2016-03-21 01:50:06,659 job 23 ended (finish() executed in (46430.736 ms)) ``` Commit: 1543f0d925075ca1058e7bca48361a97be9bd557 https://github.com/galaxyproject/galaxy/commit/1543f0d925075ca1058e7bca4836… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1959 from jmchilton/optimize_dataset_collection_discovery Optimization for discovering datasets for dynamic output collection. Compare: https://github.com/galaxyproject/galaxy/compare/497cd024da56...1543f0d92507

1 0

[galaxyproject/galaxy] 89e6a3: Add IUC as a new default bioconda channel
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89e6a37d43d85ffd46a786e689e5b2fdc6a6c4ae https://github.com/galaxyproject/galaxy/commit/89e6a37d43d85ffd46a786e689e5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add IUC as a new default bioconda channel Commit: 497cd024da56f756fd73d31d68b462ac4aee77e9 https://github.com/galaxyproject/galaxy/commit/497cd024da56f756fd73d31d68b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #1950 from galaxyproject/iuc_default_conda_channel Add IUC as a new default bioconda channel Compare: https://github.com/galaxyproject/galaxy/compare/6bd8aff0b51f...497cd024da56

1 0

[galaxyproject/galaxy] 9f2e0a: Add new generic GIE launcher
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f2e0a4c25e4bf3b4658b45f3967d53273e0675d https://github.com/galaxyproject/galaxy/commit/9f2e0a4c25e4bf3b4658b45f3967… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample A config/plugins/visualizations/gie-launcher/config/gie-launcher.xml A config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Add new generic GIE launcher Commit: 5e9a93dc9a14685225d5924b27b2c1c984e654bf https://github.com/galaxyproject/galaxy/commit/5e9a93dc9a14685225d5924b27b2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Rename based on updated allowed_images spec Commit: 43b646ccdf8ebc164c0da3f9a5e7bd3b4bfa184e https://github.com/galaxyproject/galaxy/commit/43b646ccdf8ebc164c0da3f9a5e7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Update config files Commit: 70de48d157bf278db80a71341ccb34ff4baadf63 https://github.com/galaxyproject/galaxy/commit/70de48d157bf278db80a71341ccb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Update GIE mako files to handle new image stuff Commit: 170e2652cec0ec9c78bbb62e63aa5a3ddae52d2c https://github.com/galaxyproject/galaxy/commit/170e2652cec0ec9c78bbb62e63aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Whitespace Commit: 70375af7f4e1552392e71fcc25bd0fd6d6de8279 https://github.com/galaxyproject/galaxy/commit/70375af7f4e1552392e71fcc25bd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Correct ini->txt, better menu formatting Commit: f7d92e3fc69ef4a243dd928e9ce353ae6ed7cb7f https://github.com/galaxyproject/galaxy/commit/f7d92e3fc69ef4a243dd928e9ce3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample R config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample A config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- More renames, add bam_iobio Commit: a326ce6a6fff086bd95db6a4d24cf595ec7ac1e7 https://github.com/galaxyproject/galaxy/commit/a326ce6a6fff086bd95db6a4d24c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Last ini->txt Commit: afe26640234ccc39d168c68f2216913a1ce0e268 https://github.com/galaxyproject/galaxy/commit/afe26640234ccc39d168c68f2216… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Handle incoming additional_dataset_ids Commit: e32fa927232f029aa2f6fb822349f15f46a915ed https://github.com/galaxyproject/galaxy/commit/e32fa927232f029aa2f6fb822349… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/config/gie-launcher.xml Log Message: ----------- More datatypes Commit: 8fbe7ff2b0a4f3acde8f19823f40b3319dcba371 https://github.com/galaxyproject/galaxy/commit/8fbe7ff2b0a4f3acde8f19823f40… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove debugging statement Commit: fe0702e5bdc6843444e7cf1d186fb8efee155e5f https://github.com/galaxyproject/galaxy/commit/fe0702e5bdc6843444e7cf1d186f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Nicer help text Commit: 6c2305099f3826a21bf558eb8d57c33854fe57f8 https://github.com/galaxyproject/galaxy/commit/6c2305099f3826a21bf558eb8d57… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample Log Message: ----------- Adjust jupyter to support new spec Commit: 3410dad5b1c526ff153fd0e8fd27ac7790fe0502 https://github.com/galaxyproject/galaxy/commit/3410dad5b1c526ff153fd0e8fd27… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Update jupyter launch command Commit: 29b984ea404fd0038bebc674b72d60784523a2e2 https://github.com/galaxyproject/galaxy/commit/29b984ea404fd0038bebc674b72d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Document launch command Commit: 7a0f74af2a03f8f18d92f5212cea0c203a6340dd https://github.com/galaxyproject/galaxy/commit/7a0f74af2a03f8f18d92f5212cea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Make travis happy Commit: eaf758805af03811b09d86459697855ed3e3230a https://github.com/galaxyproject/galaxy/commit/eaf758805af03811b09d86459697… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample Log Message: ----------- Correct allowed_images file for bam iobio Commit: 6155d2768d24809c0f5bbb1e5cc402ec5e55054c https://github.com/galaxyproject/galaxy/commit/6155d2768d24809c0f5bbb1e5cc4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample Log Message: ----------- Correct allowed_images file for jupyter Commit: 9192c115836a6f0f534847fcdc1297636442cbe2 https://github.com/galaxyproject/galaxy/commit/9192c115836a6f0f534847fcdc12… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako Log Message: ----------- Revert bam iobio Commit: 55bde3867250798b612568559d2b3a08480d4c65 https://github.com/galaxyproject/galaxy/commit/55bde3867250798b612568559d2b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: R config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample M config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample Log Message: ----------- Add textual descriptions to each image Commit: 69fc2f611208dd440e12f6dceea7cd0879972f5e https://github.com/galaxyproject/galaxy/commit/69fc2f611208dd440e12f6dceea7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support image descriptions Commit: d9be7fbda7944dc8b9f722c5df8fa95c5885c26a https://github.com/galaxyproject/galaxy/commit/d9be7fbda7944dc8b9f722c5df8f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample A config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample R config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample R config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- Reformat txt to yml files Commit: 351b28d46dfb08fc9e8e6646254b7fc0ca828512 https://github.com/galaxyproject/galaxy/commit/351b28d46dfb08fc9e8e6646254b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M .gitignore Log Message: ----------- Stop ignoring plugins in config Commit: 7d81e2014cba0ba21ef6cdde761bf3c38b3681fb https://github.com/galaxyproject/galaxy/commit/7d81e2014cba0ba21ef6cdde761b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M .gitignore Log Message: ----------- However, do keep ignoring locally adjusted confs Commit: c67cbe7e2717fd1b41b606d70fbf2dff7c2fd73d https://github.com/galaxyproject/galaxy/commit/c67cbe7e2717fd1b41b606d70fbf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Reconfigure plugin for yaml Commit: 4414b8acbd896cf52e0a9c8f6a51fe25786f19a7 https://github.com/galaxyproject/galaxy/commit/4414b8acbd896cf52e0a9c8f6a51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Disallow newlines Commit: f29db6e30e4a06f5bb1f98c310606d226635b17c https://github.com/galaxyproject/galaxy/commit/f29db6e30e4a06f5bb1f98c31060… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Add button for GIEs Commit: 5a6d2361f7a74fd647881851766323bd606a4ddb https://github.com/galaxyproject/galaxy/commit/5a6d2361f7a74fd6478818517663… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: R config/plugins/visualizations/gie-launcher/config/gie-launcher.xml R config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Remove custom viz plugin Commit: 590b75597edfec2833ede51b3c797dfe02edba3c https://github.com/galaxyproject/galaxy/commit/590b75597edfec2833ede51b3c79… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py A templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Move viz plugin into templates and lib Commit: 28172499d9ef2fbb3cb2f5bc5930c7f5049a0abd https://github.com/galaxyproject/galaxy/commit/28172499d9ef2fbb3cb2f5bc5930… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M static/maps/layout/menu.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/menu.js Log Message: ----------- Update bundle Commit: ba6b06cecbdff806775ed6491fd542aea18d3dea https://github.com/galaxyproject/galaxy/commit/ba6b06cecbdff806775ed6491fd5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js 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/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.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-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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-libraryrow-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less R client/galaxy/style/less/masthead.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/icon-btn.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml A config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/Gruntfile.js R config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M doc/source/project/organization.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py A lib/galaxy/tools/parameters/wrapped_json.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/wrappers.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/ucsc.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/remote_files.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M requirements.txt M run.sh M run_tests.sh M scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh R scripts/set_metadata.py R set_metadata.sh M static/maps/galaxy.library.js.map A static/maps/galaxy.menu.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map R static/maps/libs/backbone/backbone.js.map A static/maps/libs/bootstrap-tour.js.map R static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-li-edit.js.map 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/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.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/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.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-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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-libraryrow-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-template.js.map M static/maps/mvc/tool/tools.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/maps/utils/utils.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/galaxy.library.js A static/scripts/galaxy.menu.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js R static/scripts/libs/backbone/backbone.js A static/scripts/libs/bootstrap-tour.js R static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-li-edit.js 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/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.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-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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-libraryrow-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-template.js M static/scripts/mvc/tool/tools.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js M static/scripts/utils/utils.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css M static/style/blue/library.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/grid_base.mako M templates/js-app.mako M templates/show_params.mako M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/helpers.py M test/api/test_tools.py A test/api/test_tours.py A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/twilltestcase.py M test/casperjs/api-tool-tests.js M test/casperjs/casperjs_runner.py M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js M test/docker/base/run_test_wrapper.sh M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml A test/functional/tools/inputs_as_json.xml M test/functional/tools/output_action_change_format.xml M test/functional/tools/output_format.xml A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py A test/unit/managers/test_HDCAManager.py A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_routes.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/linkToDavid.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge in master Commit: 05171a7bc5334d17988751cd52fb7b930566b599 https://github.com/galaxyproject/galaxy/commit/05171a7bc5334d17988751cd52fb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M static/scripts/layout/menu.js M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correct URL, fix compiled artefact Commit: 159d689b5eb41ef749ea4ddc264759710ee6f7bc https://github.com/galaxyproject/galaxy/commit/159d689b5eb41ef749ea4ddc2647… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correctly launch with dataset_id Commit: 65beb5f4b3d9acfef3c1e224f2fb8ad805f02bcb https://github.com/galaxyproject/galaxy/commit/65beb5f4b3d9acfef3c1e224f2fb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correct text on dataset selector, hide deleted Commit: 241335539d84aec270ba7ef6c41b7c2854535ebb https://github.com/galaxyproject/galaxy/commit/241335539d84aec270ba7ef6c41b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Make use of available methods, correct ID Commit: 4bf14db042adb771888662dd4d3cf1ceb74f5cf0 https://github.com/galaxyproject/galaxy/commit/4bf14db042adb771888662dd4d3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct the format statement for mounting Commit: efcbfe6a0cc9fa882ea0e94fdf021de799993e0e https://github.com/galaxyproject/galaxy/commit/efcbfe6a0cc9fa882ea0e94fdf02… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Make flake8 happy Commit: cf4c1539df29ecd7e38c7ece351a1a31271dd170 https://github.com/galaxyproject/galaxy/commit/cf4c1539df29ecd7e38c7ece351a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Improved logic for determining if something is a GIE directory. Commit: 74eb31976318d8461bea0a0ad412f73faec00154 https://github.com/galaxyproject/galaxy/commit/74eb31976318d8461bea0a0ad412… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample Log Message: ----------- Remove ipython config, GIE has been removed in 16.04. Commit: 877c925190915ad75072d568288a22b940dbd80f https://github.com/galaxyproject/galaxy/commit/877c925190915ad75072d568288a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixup sample comments. Commit: be23cdb7190506ec03fb4bdc99b9fa9cab825bfd https://github.com/galaxyproject/galaxy/commit/be23cdb7190506ec03fb4bdc99b9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #13 from jmchilton/gie-generic-fixes Two fixes to gie generic stuff.. Commit: 95b31b63361c3140af2e8b170a764d8c1740fd15 https://github.com/galaxyproject/galaxy/commit/95b31b63361c3140af2e8b170a76… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #14 from jmchilton/gie-generic-fixes Fixup sample comments. Commit: fd28b812ef4bd8ec726a72f07d50998b35fb677c https://github.com/galaxyproject/galaxy/commit/fd28b812ef4bd8ec726a72f07d50… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Address @jmchilton's issue Commit: e62befe93b6896ab4c456e9bb5b21a47de3523f1 https://github.com/galaxyproject/galaxy/commit/e62befe93b6896ab4c456e9bb5b2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge remote-tracking branch 'origin/gie-generic' into gie-generic Commit: 0bf363517c4a362becf6edcf0c86a064a5aff559 https://github.com/galaxyproject/galaxy/commit/0bf363517c4a362becf6edcf0c86… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/style/blue/base.css M test/tool_shed/base/twilltestcase.py M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Repack artefacts, merge dev Commit: 50770c962a3018c3b3a06f0b3faab0f9ed4d1d14 https://github.com/galaxyproject/galaxy/commit/50770c962a3018c3b3a06f0b3faa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Repack client Commit: 755465cf949e96f1d97b7d1e8ca1a4924b4dae6e https://github.com/galaxyproject/galaxy/commit/755465cf949e96f1d97b7d1e8ca1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/grunt-tasks/style.js M client/package.json M config/galaxy.ini.sample M config/tool_conf.xml.main M create_db.sh M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.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/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M tools/data_source/upload.py Log Message: ----------- Merge in master Commit: 1c94fdd528ad540a1291015c044f131816d7368c https://github.com/galaxyproject/galaxy/commit/1c94fdd528ad540a1291015c044f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/modules.py M lib/tool_shed/tool_shed_registry.py M static/maps/layout/menu.js.map 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/display.mako M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge in master Commit: cc9aee6fc8b4b89e2aa318661dbc4381b8039077 https://github.com/galaxyproject/galaxy/commit/cc9aee6fc8b4b89e2aa318661dbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix to gie-generic. Commit: 51e722468383ffcf2e63e2e1ff01b8a0beec6885 https://github.com/galaxyproject/galaxy/commit/51e722468383ffcf2e63e2e1ff01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #15 from jmchilton/gie-generic A fix to my previous fix. Commit: aee38feeb4d3017cb1d0edc209bd1924c6a2cd32 https://github.com/galaxyproject/galaxy/commit/aee38feeb4d3017cb1d0edc209bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M Makefile M README.rst M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample A display_applications/biom/biom_simple.xml M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M doc/source/releases/index.rst M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/base.py M lib/galaxy/model/__init__.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/common_startup.sh M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/base/base_panels.mako M templates/sharing_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0450_skip_tool_tests.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py A test/shed_functional/functional/test_0530_repository_admin_feature.py A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_1000_install_basic_repository.py A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_1060_install_repository_with_workflow.py A test/shed_functional/functional/test_1070_invalid_tool.py A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1300_reset_all_metadata.py A test/shed_functional/functional/test_1400_review_migration_stages.py A test/shed_functional/functional/test_1410_update_manager.py A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py A test/shed_functional/functional/test_1430_repair_installed_repository.py A test/shed_functional/functional/test_1440_missing_env_sh_files.py A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py A test/shed_functional/functional/test_1460_data_managers.py A test/shed_functional/functional/test_1470_updating_installed_repositories.py A test/shed_functional/functional_tests.py A test/shed_functional/test_data/0460_files/repository_dependencies.xml A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar A test/shed_functional/test_data/0460_files/tool_dependencies.xml A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar A test/shed_functional/test_data/0480_files/tool_dependencies.xml A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar A test/shed_functional/test_data/bismark/bismark.tar A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml A test/shed_functional/test_data/blast/blast_datatypes.tar A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar A test/shed_functional/test_data/bwa/bwa_base.tar A test/shed_functional/test_data/bwa/bwa_color.tar A test/shed_functional/test_data/bwa/complex/bwa_base.tar A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml A test/shed_functional/test_data/column_maker/column_maker.tar A test/shed_functional/test_data/convert_chars/convert_chars.tar A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/shed_functional/test_data/emboss/emboss.tar A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/filtering/README A test/shed_functional/test_data/filtering/filtering_0000.txt A test/shed_functional/test_data/filtering/filtering_1.1.0.tar A test/shed_functional/test_data/filtering/filtering_2.2.0.tar A test/shed_functional/test_data/filtering/filtering_test_data.tar A test/shed_functional/test_data/filtering/readme.txt A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga A test/shed_functional/test_data/freebayes/freebayes.tar A test/shed_functional/test_data/freebayes/freebayes.xml A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample A test/shed_functional/test_data/freebayes/tool_dependencies.xml A test/shed_functional/test_data/htseq_count/htseq_count.tar A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R test/tool_shed/functional/test_0020_basic_repository_dependencies.py R test/tool_shed/functional/test_0030_repository_dependency_revisions.py R test/tool_shed/functional/test_0040_repository_circular_dependencies.py R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_0060_workflows.py R test/tool_shed/functional/test_0070_invalid_tool.py R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py R test/tool_shed/functional/test_0090_tool_search.py R test/tool_shed/functional/test_0100_complex_repository_dependencies.py R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_0130_datatype_converters.py R test/tool_shed/functional/test_0140_tool_help_images.py R test/tool_shed/functional/test_0150_prior_installation_required.py R test/tool_shed/functional/test_0160_circular_prior_installation_required.py R test/tool_shed/functional/test_0170_complex_prior_installation_required.py R test/tool_shed/functional/test_0300_reset_all_metadata.py R test/tool_shed/functional/test_0310_hg_push_from_api.py R test/tool_shed/functional/test_0400_repository_component_reviews.py R test/tool_shed/functional/test_0410_repository_component_review_access_control.py R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py R test/tool_shed/functional/test_0430_browse_utilities.py R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py R test/tool_shed/functional/test_0450_skip_tool_tests.py R test/tool_shed/functional/test_0460_upload_to_repository.py R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py R test/tool_shed/functional/test_0490_export_import_repositories.py R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py R test/tool_shed/functional/test_0530_repository_admin_feature.py R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py R test/tool_shed/functional/test_1000_install_basic_repository.py R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_1060_install_repository_with_workflow.py R test/tool_shed/functional/test_1070_invalid_tool.py R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_prior_installation_required.py R test/tool_shed/functional/test_1180_circular_prior_installation_required.py R test/tool_shed/functional/test_1190_complex_prior_installation_required.py R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1300_reset_all_metadata.py R test/tool_shed/functional/test_1400_review_migration_stages.py R test/tool_shed/functional/test_1410_update_manager.py R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py R test/tool_shed/functional/test_1430_repair_installed_repository.py R test/tool_shed/functional/test_1440_missing_env_sh_files.py R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py R test/tool_shed/functional/test_1460_data_managers.py R test/tool_shed/functional/test_1470_updating_installed_repositories.py R test/tool_shed/functional_tests.py R test/tool_shed/test_data/0460_files/repository_dependencies.xml R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar R test/tool_shed/test_data/0460_files/tool_dependencies.xml R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar R test/tool_shed/test_data/0480_files/tool_dependencies.xml R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar R test/tool_shed/test_data/bismark/bismark.tar R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml R test/tool_shed/test_data/blast/blast_datatypes.tar R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar R test/tool_shed/test_data/bwa/bwa_base.tar R test/tool_shed/test_data/bwa/bwa_color.tar R test/tool_shed/test_data/bwa/complex/bwa_base.tar R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml R test/tool_shed/test_data/column_maker/column_maker.tar R test/tool_shed/test_data/convert_chars/convert_chars.tar R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml R test/tool_shed/test_data/emboss/emboss.tar R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_lazy_process.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py A tool-data/biom_simple_display.loc.sample Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into gie-generic Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: 6bd8aff0b51ffbe07eef14d871da08fb0b76267e https://github.com/galaxyproject/galaxy/commit/6bd8aff0b51ffbe07eef14d871da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample 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/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.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/menu.js A templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Merge pull request #1403 from erasche/gie-generic Generic GIE Launcher, GIE Image Chooser, multiple datasets Compare: https://github.com/galaxyproject/galaxy/compare/3bd802268dc4...6bd8aff0b51f

1 0

[galaxyproject/galaxy] 4da9f7: Fix fluent query log serialization when datetime t...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4da9f70b39269e309d249c5bf44d2ff34cc16aa6 https://github.com/galaxyproject/galaxy/commit/4da9f70b39269e309d249c5bf44d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix fluent query log serialization when datetime types are in use. Currently queries which have raw datetime.datetime objects in the context will fail to log and throw an exception. Commit: 3bd802268dc4f024d1ea17a4721c51bd0a6d8960 https://github.com/galaxyproject/galaxy/commit/3bd802268dc4f024d1ea17a4721c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Merge pull request #2039 from dannon/fluent_tweaks Fix fluent query log serialization when datetime types are in use. Compare: https://github.com/galaxyproject/galaxy/compare/6227156d7f57...3bd802268dc4

1 0

[galaxyproject/galaxy] 46e430: Fix pbs runner file touch.
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46e4308f7c68bd83a21b425bf0ea50d285e52840 https://github.com/galaxyproject/galaxy/commit/46e4308f7c68bd83a21b425bf0ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Fix pbs runner file touch. Commit: 6227156d7f57318df5899dc0911bd299320f04f9 https://github.com/galaxyproject/galaxy/commit/6227156d7f57318df5899dc0911b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Merge pull request #2074 from dannon/pbs_fix Fix pbs runner file touch. Compare: https://github.com/galaxyproject/galaxy/compare/e7d4bc306382...6227156d7f57

1 0

[galaxyproject/galaxy] 55074c: Add Phinch as an external display application. Cur...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55074c8f33ae27246ffbe7de7f29697078458985 https://github.com/galaxyproject/galaxy/commit/55074c8f33ae27246ffbe7de7f29… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/biom/biom_simple.xml A tool-data/biom_simple_display.loc.sample Log Message: ----------- Add Phinch as an external display application. Currently linking to a personal copy of Phinch, since it requires https://github.com/PitchInteractiveInc/Phinch/pull/54 Commit: e7d4bc306382b1a077cc7e4ed54e0b0be5f42a62 https://github.com/galaxyproject/galaxy/commit/e7d4bc306382b1a077cc7e4ed54e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/biom/biom_simple.xml A tool-data/biom_simple_display.loc.sample Log Message: ----------- Merge pull request #2069 from blankenberg/biom-phinch Add Phinch as an external display application. Compare: https://github.com/galaxyproject/galaxy/compare/3ecd4e94cf1f...e7d4bc306382

1 0

[galaxyproject/galaxy] 0609fe: Need to make changes to consolidate sharing.mako f...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0609fe056f360e8f1eb6f542ee32bd1c89522c3d https://github.com/galaxyproject/galaxy/commit/0609fe056f360e8f1eb6f542ee32… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Need to make changes to consolidate sharing.mako file Commit: 2c4cb334c0b215c23e617a035f2b2062f10afa1d https://github.com/galaxyproject/galaxy/commit/2c4cb334c0b215c23e617a035f2b… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Making a single mako file for sharing and export. "sharing_base.mako" also needs to be re written. Commit: 20ef047dc150f361328d393edfe64e6556aaa0ff https://github.com/galaxyproject/galaxy/commit/20ef047dc150f361328d393edfe6… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- more mako mixing Commit: d402df68822bafa3fd6b21e61f7eb99da07e45e8 https://github.com/galaxyproject/galaxy/commit/d402df68822bafa3fd6b21e61f7e… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/sharing_base.mako M templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- more changes in sharing.mako Commit: ebda79c2ebbc88370d80ee32029149f831f4f3d6 https://github.com/galaxyproject/galaxy/commit/ebda79c2ebbc88370d80ee320291… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Scrolly fix Commit: f526a7c2b438b3a1781e92c52826d448563ac71e https://github.com/galaxyproject/galaxy/commit/f526a7c2b438b3a1781e92c52826… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #1 from dannon/workflow_sharing_menu Scrolly fix Commit: ccbc3e0045d0e46460004fe8b6c4123b837491f9 https://github.com/galaxyproject/galaxy/commit/ccbc3e0045d0e46460004fe8b6c4… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- This commit addresses issue #1782 and simplifies the workflow sharing/publish and Download/Export options Commit: 0ea13c957a6efbb7812f828e1f550eb676659a2f https://github.com/galaxyproject/galaxy/commit/0ea13c957a6efbb7812f828e1f55… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/list.mako Log Message: ----------- cleaning comments Commit: 827d175e431b9f2344293d3de47ac663cb56f17b https://github.com/galaxyproject/galaxy/commit/827d175e431b9f2344293d3de47a… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- removed commeted code Commit: dbfa39e3618bfc7706eac8108faa768d659a07f6 https://github.com/galaxyproject/galaxy/commit/dbfa39e3618bfc7706eac8108faa… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Made some small UI fixes as suggested by @martenson Commit: 4618e4cb87d2035d52c2b0022859d4951d945931 https://github.com/galaxyproject/galaxy/commit/4618e4cb87d2035d52c2b0022859… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- removed descriptions Commit: 36a8eb27eca34b0bfb6fc7106b61b3571b91949e https://github.com/galaxyproject/galaxy/commit/36a8eb27eca34b0bfb6fc7106b61… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- styling changes to share and download page hide myexperiment export as it does not work now Commit: dd2d62065c817008368df8fce094af3a6da993a8 https://github.com/galaxyproject/galaxy/commit/dd2d62065c817008368df8fce094… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- re-add my experiment export; some styling tweaks Commit: a3a2e0d07b7154839b9375e31b9fcc935f88fd06 https://github.com/galaxyproject/galaxy/commit/a3a2e0d07b7154839b9375e31b9f… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #3 from martenson/workflow_changes styling changes to share and download page Commit: 5939b6d6952df9602d1294a81d13ca44dc33dfb9 https://github.com/galaxyproject/galaxy/commit/5939b6d6952df9602d1294a81d13… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- restyle the sharing page template a bit more Commit: 263e7b28495f7975787d6f868a1bf891293948f1 https://github.com/galaxyproject/galaxy/commit/263e7b28495f7975787d6f868a1b… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #4 from martenson/workflow_changes more style Workflow changes Commit: 1ca33b1d5dbac64fc0607b974be249718869e5a4 https://github.com/galaxyproject/galaxy/commit/1ca33b1d5dbac64fc0607b974be2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- sharing page cleanup; remove invalid html tags; indentation Commit: 0abd920d0bb389a670e0f3ad943d73386f63e09e https://github.com/galaxyproject/galaxy/commit/0abd920d0bb389a670e0f3ad943d… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #5 from martenson/workflow_changes sharing page cleanup; remove invalid html tags; indentation Commit: 3ecd4e94cf1f310d09ece4b69369b4340891c3d7 https://github.com/galaxyproject/galaxy/commit/3ecd4e94cf1f310d09ece4b69369… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/sharing_base.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2060 from nitesh1989/workflow_sharing_menu Simplify Workflow sharing menu Compare: https://github.com/galaxyproject/galaxy/compare/463de48d7fdb...3ecd4e94cf1f

1 0

[galaxyproject/galaxy] 20f61e: workaround for error message in case original tool...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Compare: https://github.com/galaxyproject/galaxy/compare/90b95dc665bd...65a7ebee2336

1 0

[galaxyproject/galaxy] 7ae007: Add the Roadmap of the project
by GitHub 03 Apr '16

03 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ae007bf435820217822d945be50fa639f589628 https://github.com/galaxyproject/galaxy/commit/7ae007bf435820217822d945be50… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Add the Roadmap of the project I was reading an article from Trello: http://blog.trello.com/tips-for-making-a-public-roadmap/ and thought it could be useful for people to have direct access to the roadmap instead of looking for it in the issues. :) Commit: 114ef7336944e2e256936cc1d02d1befc9e80e40 https://github.com/galaxyproject/galaxy/commit/114ef7336944e2e256936cc1d02d… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Update README.rst Commit: 463de48d7fdbfebaf4cc7215b2c3c95ae0656818 https://github.com/galaxyproject/galaxy/commit/463de48d7fdbfebaf4cc7215b2c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Merge pull request #2071 from remimarenco/patch-4 Add the Roadmap of the project Compare: https://github.com/galaxyproject/galaxy/compare/e3cbc63def36...463de48d7fdb

1 0

[galaxyproject/galaxy] b3881f: For non-shed tool data - read loc from sample if a...
by GitHub 02 Apr '16

02 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3881f86c1fcbb98405d5a316baaf99f247ae741 https://github.com/galaxyproject/galaxy/commit/b3881f86c1fcbb98405d5a316baa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/data/__init__.py M scripts/common_startup.sh Log Message: ----------- For non-shed tool data - read loc from sample if available. Commit: e3cbc63def3607fb7a0a646000d2b12ed728a579 https://github.com/galaxyproject/galaxy/commit/e3cbc63def3607fb7a0a646000d2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-02 (Sat, 02 Apr 2016) Changed paths: M lib/galaxy/tools/data/__init__.py M scripts/common_startup.sh Log Message: ----------- Merge pull request #2070 from jmchilton/tool_loc_sample For non-shed tool data - read loc from sample if available. Compare: https://github.com/galaxyproject/galaxy/compare/e02e97dc798d...e3cbc63def36

1 0