[galaxy-commits] [galaxyproject/galaxy] 9f2e0a: Add new generic GIE launcher

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f2e0a4c25e4bf3b4658b45f3967d53273e0675d https://github.com/galaxyproject/galaxy/commit/9f2e0a4c25e4bf3b4658b45f3967d... Author: Eric Rasche <rasche.eric@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/5e9a93dc9a14685225d5924b27b2c... Author: Eric Rasche <rasche.eric@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/43b646ccdf8ebc164c0da3f9a5e7b... Author: Eric Rasche <rasche.eric@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/70de48d157bf278db80a71341ccb3... Author: Eric Rasche <rasche.eric@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/170e2652cec0ec9c78bbb62e63aa5... Author: Eric Rasche <rasche.eric@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/70375af7f4e1552392e71fcc25bd0... Author: Eric Rasche <rasche.eric@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/f7d92e3fc69ef4a243dd928e9ce35... Author: Eric Rasche <rasche.eric@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/a326ce6a6fff086bd95db6a4d24cf... Author: Eric Rasche <rasche.eric@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/afe26640234ccc39d168c68f22169... Author: Eric Rasche <rasche.eric@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/e32fa927232f029aa2f6fb822349f... Author: Eric Rasche <rasche.eric@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/8fbe7ff2b0a4f3acde8f19823f40b... Author: Eric Rasche <rasche.eric@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/fe0702e5bdc6843444e7cf1d186fb... Author: Eric Rasche <rasche.eric@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/6c2305099f3826a21bf558eb8d57c... Author: Eric Rasche <rasche.eric@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/3410dad5b1c526ff153fd0e8fd27a... Author: Eric Rasche <rasche.eric@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/29b984ea404fd0038bebc674b72d6... Author: Eric Rasche <rasche.eric@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/7a0f74af2a03f8f18d92f5212cea0... Author: Eric Rasche <rasche.eric@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/eaf758805af03811b09d864596978... Author: Eric Rasche <rasche.eric@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/6155d2768d24809c0f5bbb1e5cc40... Author: Eric Rasche <rasche.eric@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/9192c115836a6f0f534847fcdc129... Author: Eric Rasche <rasche.eric@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/55bde3867250798b612568559d2b3... Author: Eric Rasche <rasche.eric@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/69fc2f611208dd440e12f6dceea7c... Author: Eric Rasche <rasche.eric@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/d9be7fbda7944dc8b9f722c5df8fa... Author: Eric Rasche <rasche.eric@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/351b28d46dfb08fc9e8e6646254b7... Author: Eric Rasche <rasche.eric@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/7d81e2014cba0ba21ef6cdde761bf... Author: Eric Rasche <rasche.eric@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/c67cbe7e2717fd1b41b606d70fbf2... Author: Eric Rasche <rasche.eric@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/4414b8acbd896cf52e0a9c8f6a51f... Author: Eric Rasche <rasche.eric@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/f29db6e30e4a06f5bb1f98c310606... Author: Eric Rasche <rasche.eric@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/5a6d2361f7a74fd64788185176632... Author: Eric Rasche <rasche.eric@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/590b75597edfec2833ede51b3c797... Author: Eric Rasche <rasche.eric@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/28172499d9ef2fbb3cb2f5bc5930c... Author: Eric Rasche <rasche.eric@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/ba6b06cecbdff806775ed6491fd54... 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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 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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/05171a7bc5334d17988751cd52fb7... Author: Eric Rasche <rasche.eric@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/159d689b5eb41ef749ea4ddc26475... Author: Eric Rasche <rasche.eric@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/65beb5f4b3d9acfef3c1e224f2fb8... Author: Eric Rasche <rasche.eric@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/241335539d84aec270ba7ef6c41b7... Author: Eric Rasche <rasche.eric@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/4bf14db042adb771888662dd4d3cf... Author: Eric Rasche <rasche.eric@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/efcbfe6a0cc9fa882ea0e94fdf021... Author: Eric Rasche <rasche.eric@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/cf4c1539df29ecd7e38c7ece351a1... Author: John Chilton <jmchilton@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/74eb31976318d8461bea0a0ad412f... Author: John Chilton <jmchilton@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/877c925190915ad75072d568288a2... Author: John Chilton <jmchilton@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/be23cdb7190506ec03fb4bdc99b9f... Author: Eric Rasche <rasche.eric@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/95b31b63361c3140af2e8b170a764... Author: Eric Rasche <rasche.eric@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/fd28b812ef4bd8ec726a72f07d509... Author: Eric Rasche <rasche.eric@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/e62befe93b6896ab4c456e9bb5b21... Author: Eric Rasche <rasche.eric@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/0bf363517c4a362becf6edcf0c86a... 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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/1c94fdd528ad540a1291015c044f1... Author: Eric Rasche <rasche.eric@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/cc9aee6fc8b4b89e2aa318661dbc4... Author: John Chilton <jmchilton@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/51e722468383ffcf2e63e2e1ff01b... Author: John Chilton <jmchilton@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/aee38feeb4d3017cb1d0edc209bd1... Author: John Chilton <jmchilton@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 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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/6bd8aff0b51ffbe07eef14d871da0... Author: John Chilton <jmchilton@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