- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 85aaa2: Make conda install and resolver status more robust
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 85aaa23785ff10337b40d9a5f4316e8a4683668d https://github.com/galaxyproject/galaxy/commit/85aaa23785ff10337b40d9a5f431… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Make conda install and resolver status more robust We disable the conda resolver if conda_exec is not found and we are unable to install conda. Skip installing conda if it won't be used (because conda exec is outside of conda_prefix). Install conda if conda_prefix is an empty directory. Commit: fdc43a1448453afa1e65ae43f20b71865762882d https://github.com/galaxyproject/galaxy/commit/fdc43a1448453afa1e65ae43f20b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase conda options and explain conda_prefix, add current length limitation Commit: 0cc10d184dfb949130fefedfe12258241f4982c9 https://github.com/galaxyproject/galaxy/commit/0cc10d184dfb949130fefedfe122… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Move can_install_conda and is_conda_installed into CondaContext Commit: 30a14e3c392395805453f15d35b9d9c0b76a65ee https://github.com/galaxyproject/galaxy/commit/30a14e3c392395805453f15d35b9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Raise a more specific exception Commit: 40f8589c3830af3c4ca69ebcd394d9bf5a53e65b https://github.com/galaxyproject/galaxy/commit/40f8589c3830af3c4ca69ebcd394… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2789 from mvdbeek/is_conda_installed Make conda install and resolver status more robust Compare: https://github.com/galaxyproject/galaxy/compare/d87fbdd5b80b...40f8589c3830

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[galaxyproject/galaxy] af533a: Create a uWSGI postfork function registry. Also, s...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af533a7a6ff0106185350466b31153e40c394389 https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Create a uWSGI postfork function registry. Also, start the tool conf watcher thread post-fork. Commit: 7ebf7e57063624758eaea62756126fd556cfa989 https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Force update repository manager to launch postfork. Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. Commit: fb6f3c9c698a14d9f67fe6262e16c65ddc78477e https://github.com/galaxyproject/galaxy/commit/fb6f3c9c698a14d9f67fe6262e16… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- separate styles of new and old libs fixing various ui bugs Commit: 0719d83837aacf45b200709cb7b243badca87488 https://github.com/galaxyproject/galaxy/commit/0719d83837aacf45b200709cb7b2… Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2780 from martenson/lib-style-fix [16.07] separate styles of new and old libraries fixing various ui bugs Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Separates the decorator from the injected uwsgi package to fix 'process_is_uwsgi' logic. Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966 https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #4 from dannon/uwsgi-fork Force update repository manager to launch postfork. Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415 https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Words. Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584 https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge pull request #5 from dannon/uwsgi-fork Add a warning when it is detected that a process is uwsgi based but u… Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #2774 from natefoo/uwsgi-fork [16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork Commit: 62d69be1565d8d854fe8bd0a289732ec9e12001c https://github.com/galaxyproject/galaxy/commit/62d69be1565d8d854fe8bd0a2897… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/less/library.less M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py 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/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d20828b685e5...62d69be1565d

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[galaxyproject/galaxy] af533a: Create a uWSGI postfork function registry. Also, s...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: af533a7a6ff0106185350466b31153e40c394389 https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Create a uWSGI postfork function registry. Also, start the tool conf watcher thread post-fork. Commit: 7ebf7e57063624758eaea62756126fd556cfa989 https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Force update repository manager to launch postfork. Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Separates the decorator from the injected uwsgi package to fix 'process_is_uwsgi' logic. Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966 https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #4 from dannon/uwsgi-fork Force update repository manager to launch postfork. Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415 https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Words. Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584 https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge pull request #5 from dannon/uwsgi-fork Add a warning when it is detected that a process is uwsgi based but u… Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #2774 from natefoo/uwsgi-fork [16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork Compare: https://github.com/galaxyproject/galaxy/compare/0719d83837aa...d87fbdd5b80b

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[galaxyproject/galaxy] 78c58f: Add column names to BED datatype so that column na...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c58f00f7eb69229e4f3a03130fa07434e4c154 https://github.com/galaxyproject/galaxy/commit/78c58f00f7eb69229e4f3a03130f… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Add column names to BED datatype so that column names are displayed in dataset viewer. Commit: d20828b685e5d70fcf2c15b4fc7555be60d446e9 https://github.com/galaxyproject/galaxy/commit/d20828b685e5d70fcf2c15b4fc75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #2784 from jgoecks/bed_col_names Add column names to BED datatype so that column names are displayed i… Compare: https://github.com/galaxyproject/galaxy/compare/6fb006c460da...d20828b685e5

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[galaxyproject/galaxy] 87038d: Ensure proper filtering of dataset when injecting ...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87038d275acf46d84c1c8c110742a44002b6bdf3 https://github.com/galaxyproject/galaxy/commit/87038d275acf46d84c1c8c110742… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Ensure proper filtering of dataset when injecting input data on workflow initialization Commit: e614a6e6e4300d361d8b861a733e312f82e59b5a https://github.com/galaxyproject/galaxy/commit/e614a6e6e4300d361d8b861a733e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Improve initial value injection, adjust former run form Commit: 6fb006c460daca657a429ae78e63add6c48ef151 https://github.com/galaxyproject/galaxy/commit/6fb006c460daca657a429ae78e63… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2777 from guerler/fix_filter_set Ensure proper filtering of dataset when injecting input data on workflow initialization Compare: https://github.com/galaxyproject/galaxy/compare/3b848891e5cf...6fb006c460da

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[galaxyproject/galaxy] 25d9e0: reimplement clone tracking that used to be in the ...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25d9e0905b6ac1adf837e4da407bc8a55bf098af https://github.com/galaxyproject/galaxy/commit/25d9e0905b6ac1adf837e4da407b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- reimplement clone tracking that used to be in the middleware Commit: 3b848891e5cf9abcf2063ebeb5d4d14811aec58f https://github.com/galaxyproject/galaxy/commit/3b848891e5cf9abcf2063ebeb5d4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Merge pull request #2782 from martenson/reimplement-clone-tracking reimplement clone tracking that used to be in the middleware Compare: https://github.com/galaxyproject/galaxy/compare/0dee01934a9f...3b848891e5cf

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[galaxyproject/galaxy] fb6f3c: separate styles of new and old libs fixing various...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: fb6f3c9c698a14d9f67fe6262e16c65ddc78477e https://github.com/galaxyproject/galaxy/commit/fb6f3c9c698a14d9f67fe6262e16… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- separate styles of new and old libs fixing various ui bugs Commit: 0719d83837aacf45b200709cb7b243badca87488 https://github.com/galaxyproject/galaxy/commit/0719d83837aacf45b200709cb7b2… Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2780 from martenson/lib-style-fix [16.07] separate styles of new and old libraries fixing various ui bugs Compare: https://github.com/galaxyproject/galaxy/compare/66e725b6e33b...0719d83837aa

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[galaxyproject/galaxy] b2593f: Properly refresh history contents after submitting...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2593f0ff209aaef80b82caec4ea7c8018091e87 https://github.com/galaxyproject/galaxy/commit/b2593f0ff209aaef80b82caec4ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Properly refresh history contents after submitting workflow through new scheduler Commit: 0dee01934a9f3e4cb62e005b07a3442dd815572d https://github.com/galaxyproject/galaxy/commit/0dee01934a9f3e4cb62e005b07a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #2776 from guerler/properly_refresh_after_workflow Properly refresh history contents after submitting workflow through api scheduler Compare: https://github.com/galaxyproject/galaxy/compare/0692f8b4b11d...0dee01934a9f

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[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: 66e725b6e33b9e2f1fd447fdec53f025db71e55c https://github.com/galaxyproject/galaxy/commit/66e725b6e33b9e2f1fd447fdec53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 0692f8b4b11df0ea7004e774f2ee3695293a8e6e https://github.com/galaxyproject/galaxy/commit/0692f8b4b11df0ea7004e774f2ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0f5239dd3204...0692f8b4b11d

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[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: 66e725b6e33b9e2f1fd447fdec53f025db71e55c https://github.com/galaxyproject/galaxy/commit/66e725b6e33b9e2f1fd447fdec53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/4b86f6137f13...66e725b6e33b

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[galaxyproject/galaxy] 33c402: Fix misplaced parenthesis
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 33c4025fabc057a412c2da662b3606afc0726902 https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix misplaced parenthesis Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304 Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M tox.ini Log Message: ----------- Pin flake8 version Do not pin when forward-merging to dev branch. Also ignore .tox/ and eggs/ as in #2650 . Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package [16.01] Fix misplaced parenthesis Commit: f2f62f340ecd92ebdde51e6d13d5145a6f40cc9e https://github.com/galaxyproject/galaxy/commit/f2f62f340ecd92ebdde51e6d13d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: .ci/flake8_blacklist.txt tox.ini Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: f8cf6f834bd92b82a05250b1c1f0e42957bffb15 https://github.com/galaxyproject/galaxy/commit/f8cf6f834bd92b82a05250b1c1f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/tools/parameters/basic.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/fb76aa0a938a...f8cf6f834bd9

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[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Compare: https://github.com/galaxyproject/galaxy/compare/f2f62f340ecd...ceeef39edb55

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[galaxyproject/infrastructure-playbook] b9ef8f: Add gxsrc user
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b9ef8f9b0b68955a0b4ded2e69fc8a9f262a6c1e https://github.com/galaxyproject/infrastructure-playbook/commit/b9ef8f9b0b6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml R taccenv/secret_group_vars/galaxymainservers.yml R taccenv/secret_group_vars/galaxytestservers.yml A taccenv/secret_group_vars/maingalaxyservers.yml A taccenv/secret_group_vars/testgalaxyservers.yml Log Message: ----------- Add gxsrc user

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[galaxyproject/galaxy] c60600: update
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c606003c1000cdbc171c011ccb952c444868271d https://github.com/galaxyproject/galaxy/commit/c606003c1000cdbc171c011ccb95… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/runners/godocker.py Log Message: ----------- update Commit: f68b17c5a805c7208628ec60485150fc7ccd8a88 https://github.com/galaxyproject/galaxy/commit/f68b17c5a805c7208628ec604851… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Indent Fix Commit: d626c33a131fb3634e4ed3ec2f7130969aca0b0f https://github.com/galaxyproject/galaxy/commit/d626c33a131fb3634e4ed3ec2f71… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- GoDocker runner:Indent fix Commit: 0e79c824800debc4d398ac9b2f6559d09e7c9ac9 https://github.com/galaxyproject/galaxy/commit/0e79c824800debc4d398ac9b2f65… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: A doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Add tutorial for building a runner for galaxy Commit: a6d3c54522a11d6dc467e737a65b90c47ce5c960 https://github.com/galaxyproject/galaxy/commit/a6d3c54522a11d6dc467e737a65b… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Update job_conf.xml.sample_advanced Commit: 57b2171a79c8993d57256fdbe557fe597fbc9612 https://github.com/galaxyproject/galaxy/commit/57b2171a79c8993d57256fdbe557… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: R lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Delete godocker.py Commit: 5239774fc64e164c0d8ee682d9456149194fbd74 https://github.com/galaxyproject/galaxy/commit/5239774fc64e164c0d8ee682d945… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Update Build_a_runner_for_galaxy.md Commit: 0b8060619eb1695aa1efd667f45d62fa9a0d87e1 https://github.com/galaxyproject/galaxy/commit/0b8060619eb1695aa1efd667f45d… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Update Build_a_runner_for_galaxy.md Commit: 54a019435c38d54c1e4f614ff2453907697bbb54 https://github.com/galaxyproject/galaxy/commit/54a019435c38d54c1e4f614ff245… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: R doc/source/dev/Build_a_runner_for_galaxy.md A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Convert to RST, fix image references. Commit: b0eb01cc5bf21f9d7535893b6dd34daae843ef82 https://github.com/galaxyproject/galaxy/commit/b0eb01cc5bf21f9d7535893b6dd3… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: R doc/source/dev/Build_a_runner_for_galaxy.md A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #1 from dannon/doc_dev Convert to RST, fix image references. Commit: 5e639f2bbda3145b925b2565c32e188c7caa55e8 https://github.com/galaxyproject/galaxy/commit/5e639f2bbda3145b925b2565c32e… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: dbd5c848355d12634cf3c9dbb031c29c9a2ea0ec https://github.com/galaxyproject/galaxy/commit/dbd5c848355d12634cf3c9dbb031… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: a06347102dcac5645b92b36c30433051ab6e90ea https://github.com/galaxyproject/galaxy/commit/a06347102dcac5645b92b36c3043… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: 115df2963e339b44c4dec459f19cbc706af2da92 https://github.com/galaxyproject/galaxy/commit/115df2963e339b44c4dec459f19c… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: 0f5239dd32043eef00269c3ef363c864d83c3dcc https://github.com/galaxyproject/galaxy/commit/0f5239dd32043eef00269c3ef363… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #2700 from varunshankar/doc_dev A tutorial on Build runner for galaxy Compare: https://github.com/galaxyproject/galaxy/compare/8e59a4c84c2c...0f5239dd3204

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[galaxyproject/galaxy] 069d44: Revise repeat block view, remove unecessary table ...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 069d44da36e3067668e99f84d5c756621e0eac66 https://github.com/galaxyproject/galaxy/commit/069d44da36e3067668e99f84d5c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M static/maps/mvc/form/form-repeat.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js Log Message: ----------- Revise repeat block view, remove unecessary table wrapper Commit: 8eabf568330bf7c91bff73d72a648fa4a7a09512 https://github.com/galaxyproject/galaxy/commit/8eabf568330bf7c91bff73d72a64… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Enhance test cases, add repeat block tests Commit: b6e585424ba3ff75659dde1b01e5d624af824e1a https://github.com/galaxyproject/galaxy/commit/b6e585424ba3ff75659dde1b01e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M static/maps/mvc/form/form-repeat.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/mvc/form/form-repeat.js Log Message: ----------- Remove unused table library from define/include Commit: 8e59a4c84c2c83806f7162d096d66d68cc39f0c4 https://github.com/galaxyproject/galaxy/commit/8e59a4c84c2c83806f7162d096d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.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/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #2770 from guerler/revise_repeats Revise repeat block view, remove unecessary table wrapper Compare: https://github.com/galaxyproject/galaxy/compare/f174c8bd4296...8e59a4c84c2c

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[galaxyproject/infrastructure-playbook] 3851a8: Infrastructure for new Galaxy job handler VMs
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3851a8ed924a2fc746938727a1d4f9788aaa6397 https://github.com/galaxyproject/infrastructure-playbook/commit/3851a8ed924… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: A roles/cvmfs/files/cvmfs_wipecache.centos_7 A taccenv/group_vars/slurmclients.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/slurmclients.yml A taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Infrastructure for new Galaxy job handler VMs

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[galaxyproject/galaxy] 87d623: Improve startup scripts
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87d6239c362397824f6d145b56d564dfb3d4b774 https://github.com/galaxyproject/galaxy/commit/87d6239c362397824f6d145b56d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Improve startup scripts Fix errors reported by shellcheck Commit: f174c8bd4296a7fa74d23af39cb8d0523a69aa4f https://github.com/galaxyproject/galaxy/commit/f174c8bd4296a7fa74d23af39cb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #2765 from nsoranzo/run_sh Improve startup scripts Compare: https://github.com/galaxyproject/galaxy/compare/ac5ce47888e0...f174c8bd4296

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[galaxyproject/infrastructure-playbook] d8dec9: Allow jenkins on slaves to log in to the starforge...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d8dec916e7b50acf2973e1f5081eac8e305758cf https://github.com/galaxyproject/infrastructure-playbook/commit/d8dec916e7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Allow jenkins on slaves to log in to the starforge builder

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[galaxyproject/galaxy] 893047: Rephrase comment
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89304762a21c0122659ba08a719813d7790e7a7b https://github.com/galaxyproject/galaxy/commit/89304762a21c0122659ba08a7198… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase comment Commit: a9e04331de9ba972be9d394da32439fb3054707c https://github.com/galaxyproject/galaxy/commit/a9e04331de9ba972be9d394da324… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Ensure EXIT_CODE is set. Kill Galaxy for local testing Also properly initialise $i and use POSIX syntax Commit: 4b86f6137f132eb640424194766383f39fa18f32 https://github.com/galaxyproject/galaxy/commit/4b86f6137f132eb6404241947663… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge pull request #2773 from nsoranzo/release_16.07_followup_for_2759 [16.07] Small followup for #2759 Commit: ac5ce47888e006279e94d242b8bb55b32edae529 https://github.com/galaxyproject/galaxy/commit/ac5ce47888e006279e94d242b8bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b40e9938d68b...ac5ce47888e0

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[galaxyproject/galaxy] 0bf941: Minimally functional metadata file fetching via th...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bf9417fbaf56ff52edfa62458d9f66bada6a449 https://github.com/galaxyproject/galaxy/commit/0bf9417fbaf56ff52edfa62458d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Minimally functional metadata file fetching via the API Commit: e219dfef95a565bee081ff89cb8110a860722bdd https://github.com/galaxyproject/galaxy/commit/e219dfef95a565bee081ff89cb81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Add download url for metadata file. Commit: f87b08efa0d0d2c127eab88cf31233df3e867ec1 https://github.com/galaxyproject/galaxy/commit/f87b08efa0d0d2c127eab88cf312… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Consolidate usage of 'valid_chars' in the application. Commit: ce04973b20e3c21a274f8f3560b1d2086d0d410c https://github.com/galaxyproject/galaxy/commit/ce04973b20e3c21a274f8f3560b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename get_metadata_file route to just metadata_file. Thanks @carlfeberhard. Commit: c9ac723174ae7200230575b7101c91353744e319 https://github.com/galaxyproject/galaxy/commit/c9ac723174ae7200230575b7101c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Revert genomespace tool changes related to FILENAME_VALID_CHARS Commit: b40e9938d68b3d5d2d818e178ae24e9317ee3728 https://github.com/galaxyproject/galaxy/commit/b40e9938d68b3d5d2d818e178ae2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #2741 from dannon/expose_metadata_api Metadata file fetching via the API Compare: https://github.com/galaxyproject/galaxy/compare/49f58dd01771...b40e9938d68b

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[galaxyproject/galaxy] 893047: Rephrase comment
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 89304762a21c0122659ba08a719813d7790e7a7b https://github.com/galaxyproject/galaxy/commit/89304762a21c0122659ba08a7198… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase comment Commit: a9e04331de9ba972be9d394da32439fb3054707c https://github.com/galaxyproject/galaxy/commit/a9e04331de9ba972be9d394da324… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Ensure EXIT_CODE is set. Kill Galaxy for local testing Also properly initialise $i and use POSIX syntax Commit: 4b86f6137f132eb640424194766383f39fa18f32 https://github.com/galaxyproject/galaxy/commit/4b86f6137f132eb6404241947663… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge pull request #2773 from nsoranzo/release_16.07_followup_for_2759 [16.07] Small followup for #2759 Compare: https://github.com/galaxyproject/galaxy/compare/a7be24e111de...4b86f6137f13

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[galaxyproject/galaxy] e29cf1: Add implicit conversions target extension to hda n...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e29cf1b7ee669d602995afed43122c288aef785f https://github.com/galaxyproject/galaxy/commit/e29cf1b7ee669d602995afed4312… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: 49f58dd017718ce16ee8314504ba8c52e70dcd48 https://github.com/galaxyproject/galaxy/commit/49f58dd017718ce16ee8314504ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2734 from guerler/add_implicit_conversion_info Add implicit conversions target extension to hda name when listed as selection option Compare: https://github.com/galaxyproject/galaxy/compare/4ffbedd844b0...49f58dd01771

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[galaxyproject/galaxy] 9d467d: enable conda_auto_init in sample, adjust wording
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- enable conda_auto_init in sample, adjust wording Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix string substitution Commit: 730233f48a4ba64c338969036845b0d2aeea5035 https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #15 from mvdbeek/fix_string_substitution Fix string substitution Commit: e35c6295694c4065fc880e00fabe43f0c1905748 https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Extend startup time Commit: 702891e3efc79fa75ed8e7475e712760355d825c https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Merge pull request #16 from mvdbeek/fix_string_substitution Extend startup time Commit: a7be24e111de2c37c52af580c8a776ee0478ec92 https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2759 from martenson/conda_config [16.07] install Conda at startup; enable conda_auto_init in sample conf Commit: 4ffbedd844b077b48c09092ed0d406ab73060148 https://github.com/galaxyproject/galaxy/commit/4ffbedd844b077b48c09092ed0d4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/13b8067d91f8...4ffbedd844b0

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[galaxyproject/galaxy] 9d467d: enable conda_auto_init in sample, adjust wording
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- enable conda_auto_init in sample, adjust wording Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix string substitution Commit: 730233f48a4ba64c338969036845b0d2aeea5035 https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #15 from mvdbeek/fix_string_substitution Fix string substitution Commit: e35c6295694c4065fc880e00fabe43f0c1905748 https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Extend startup time Commit: 702891e3efc79fa75ed8e7475e712760355d825c https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Merge pull request #16 from mvdbeek/fix_string_substitution Extend startup time Commit: a7be24e111de2c37c52af580c8a776ee0478ec92 https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2759 from martenson/conda_config [16.07] install Conda at startup; enable conda_auto_init in sample conf Compare: https://github.com/galaxyproject/galaxy/compare/9c03d4c16fad...a7be24e111de

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[galaxyproject/galaxy] 185924: Update python-ldap module
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 185924e45a5b413c50d3aae7e330677e34376c1b https://github.com/galaxyproject/galaxy/commit/185924e45a5b413c50d3aae7e330… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: 13b8067d91f81d8e638b89aa44ea5ba0a053dbcc https://github.com/galaxyproject/galaxy/commit/13b8067d91f81d8e638b89aa44ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2738 from abretaud/patch-1 Update python-ldap module Compare: https://github.com/galaxyproject/galaxy/compare/0052a1c3bba1...13b8067d91f8

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