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

[galaxyproject/usegalaxy-playbook] 6f4f8d: fix welcomepage tiny things
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/fix-welcome-tinies Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f4f8d4fa8691bc8f3d4d03ac048667f2b638859 https://github.com/galaxyproject/usegalaxy-playbook/commit/6f4f8d4fa8691bc8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- fix welcomepage tiny things

1 0

[galaxyproject/galaxy] 9dc9dd: Add --replace-pip option to common_startup.sh.
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9dc9ddf8cdede7c62d4ba5f00283675b872891e4 https://github.com/galaxyproject/galaxy/commit/9dc9ddf8cdede7c62d4ba5f00283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Add --replace-pip option to common_startup.sh. Needed to restore correct functionality to planemo. Commit: 8fd83df6652a40882bcc3ca8a1db917887b71c11 https://github.com/galaxyproject/galaxy/commit/8fd83df6652a40882bcc3ca8a1db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Allow override of location of virtual env Galaxy manages. Commit: becffe93a3f78ca74b5d093974844a3634e1ed6b https://github.com/galaxyproject/galaxy/commit/becffe93a3f78ca74b5d09397484… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #1485 from jmchilton/common_startup_fixes [16.01] Fix common_startup options for planemo. Compare: https://github.com/galaxyproject/galaxy/compare/86158cbc7fb6...becffe93a3f7

1 0

[galaxyproject/usegalaxy-playbook] d10cbd: Update Main, replace IPython with Jupyter
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d10cbd5443f35683bae9dcf11d41c4d972e3ca40 https://github.com/galaxyproject/usegalaxy-playbook/commit/d10cbd5443f35683… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version A production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample A production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml A production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js A production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako R production/files/interactive_environments/plugins/ipython/config/ipython.ini.sample R production/files/interactive_environments/plugins/ipython/config/ipython.xml R production/files/interactive_environments/plugins/ipython/static/js/ipython.js R production/files/interactive_environments/plugins/ipython/templates/ipython.mako R production/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample A production/files/interactive_environments/plugins/jupyter/config/jupyter.xml A production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js A production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/lib/proxy.js M production/group_vars/all.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main, replace IPython with Jupyter

1 0

[galaxyproject/usegalaxy-playbook] b3c8d7: Fix IEs on Test (IPython->Jupyter), fetch Mutable ...
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3c8d78efd762f7ca9c49ab302320245deb297f9 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3c8d78efd762f7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version R stage/files/interactive_environments/plugins/ipython/config/ipython.ini.sample R stage/files/interactive_environments/plugins/ipython/config/ipython.xml R stage/files/interactive_environments/plugins/ipython/static/js/ipython.js R stage/files/interactive_environments/plugins/ipython/templates/ipython.mako R stage/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A stage/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample A stage/files/interactive_environments/plugins/jupyter/config/jupyter.xml A stage/files/interactive_environments/plugins/jupyter/static/js/jupyter.js A stage/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/lib/proxy.js M stage/group_vars/galaxyservers.yml Log Message: ----------- Fix IEs on Test (IPython->Jupyter), fetch Mutable configs

1 0

[galaxyproject/usegalaxy-playbook] 8cd74c: update Test
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8cd74c9896d37ebd1ac0b4a2764cd43f7060e839 https://github.com/galaxyproject/usegalaxy-playbook/commit/8cd74c9896d37ebd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test

1 0

[galaxyproject/usegalaxy-playbook] 1a2b3d: fix links; change iplant name and logo
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a2b3d71b3d99fd6e34377c77b491f564da9090b https://github.com/galaxyproject/usegalaxy-playbook/commit/1a2b3d71b3d99fd6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A files/galaxy/common/static/welcome_img/cyverse_rgb_200.png R files/galaxy/common/static/welcome_img/iplant_logo.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- fix links; change iplant name and logo Commit: 5c73bec636caa728eae95a0a49cf39abd9f8c41a https://github.com/galaxyproject/usegalaxy-playbook/commit/5c73bec636caa728… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add links to get own Galaxy and tools Commit: 21defc05e52b9c9b15124de65d5af762d7f3a5cf https://github.com/galaxyproject/usegalaxy-playbook/commit/21defc05e52b9c9b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A files/galaxy/common/static/welcome_img/cyverse_rgb_200.png R files/galaxy/common/static/welcome_img/iplant_logo.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Merge pull request #15 from galaxyproject/update-welcome changes to welcomepage Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ec59c63e9ad6...…

1 0

[galaxyproject/galaxy] b559cf: Drop E731 from flake8 enforcement (though we shoul...
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b559cf303c1b14aa862ba394d7bc868bc517db5a https://github.com/galaxyproject/galaxy/commit/b559cf303c1b14aa862ba394d7bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M setup.cfg Log Message: ----------- Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) Commit: 2f1dbeee68ddd75a561fe0f463d5b9968278ef13 https://github.com/galaxyproject/galaxy/commit/2f1dbeee68ddd75a561fe0f463d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.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/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M test/casperjs/casperjs_runner.py Log Message: ----------- Address W503 and E721 errors now enforced by pep8 1.7. Commit: 86158cbc7fb601d0f3563fa2bea67e23b464db93 https://github.com/galaxyproject/galaxy/commit/86158cbc7fb601d0f3563fa2bea6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.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/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1487 from dannon/release_16.01 [16.01] Cherrypick of pep8 fixes. Compare: https://github.com/galaxyproject/galaxy/compare/24cb97cdbf96...86158cbc7fb6

1 0

[galaxyproject/usegalaxy-playbook] 1a2b3d: fix links; change iplant name and logo
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/update-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a2b3d71b3d99fd6e34377c77b491f564da9090b https://github.com/galaxyproject/usegalaxy-playbook/commit/1a2b3d71b3d99fd6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A files/galaxy/common/static/welcome_img/cyverse_rgb_200.png R files/galaxy/common/static/welcome_img/iplant_logo.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- fix links; change iplant name and logo Commit: 5c73bec636caa728eae95a0a49cf39abd9f8c41a https://github.com/galaxyproject/usegalaxy-playbook/commit/5c73bec636caa728… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add links to get own Galaxy and tools Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1a2b3d71b3d9^..…

1 0

[galaxyproject/galaxy] b47b5f: Fix for bad URL generation when empty GET string d...
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b47b5ff00a3db510bf570391d32c96aa98b316c7 https://github.com/galaxyproject/galaxy/commit/b47b5ff00a3db510bf570391d32c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map 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/utils/utils.js Log Message: ----------- Fix for bad URL generation when empty GET string data. Commit: 4819d1aa7168a29c33ca7f0bfe16e605dbb50e92 https://github.com/galaxyproject/galaxy/commit/4819d1aa7168a29c33ca7f0bfe16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- set ajaxConfig.data to null if an empty dict Commit: c4b532303576b02cffbf8ee8df63e086686d551b https://github.com/galaxyproject/galaxy/commit/c4b532303576b02cffbf8ee8df63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Remove parenthesis Commit: 46e5e480cbbf3f1ad504be4536bd24827dc5a3f4 https://github.com/galaxyproject/galaxy/commit/46e5e480cbbf3f1ad504be4536bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: 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 M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.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/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M test/casperjs/casperjs_runner.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into lparsons_bad_urls Commit: 790953e6e786199f237b287cff653a9f33b31e63 https://github.com/galaxyproject/galaxy/commit/790953e6e786199f237b287cff65… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map 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/utils/utils.js Log Message: ----------- Merge pull request #1478 from dannon/lparsons_bad_urls URL generation tweaks for utils.js Compare: https://github.com/galaxyproject/galaxy/compare/0a6f6c3da438...790953e6e786

1 0

[galaxyproject/usegalaxy-playbook] ec59c6: Bump scatterplot to 16GB, decrease multi limit on ...
by GitHub 12 Jan '16

12 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ec59c63e9ad6ba9776563d9754c5e2edbe2c1bd9 https://github.com/galaxyproject/usegalaxy-playbook/commit/ec59c63e9ad6ba97… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Bump scatterplot to 16GB, decrease multi limit on Main

1 0