Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 74afe4127a2e5d1b2e3b36fcc220866a6db02e7f
https://github.com/galaxyproject/galaxy/commit/74afe4127a2e5d1b2e3b36fcc220…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
fix old jobparam hack for importing files to library
Commit: f41550f69f05df63e762b771a22c0b677357db85
https://github.com/galaxyproject/galaxy/commit/f41550f69f05df63e762b771a22c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-14 (Thu, 14 Jan 2016)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge pull request #1488 from martenson/fix-jobparam-hack
fix old jobparam hack for importing files to library
Compare: https://github.com/galaxyproject/galaxy/compare/84fd89d67a5a...f41550f69f05
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: 4b5b970d7898a33faca5557b4382ddc9d3923ae6
https://github.com/galaxyproject/galaxy/commit/4b5b970d7898a33faca5557b4382…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M test/qunit/tests/masthead_tests.js
Log Message:
-----------
Fix disabled css
Commit: 0902c23f3491b4840b649a203315939d0c7caa8c
https://github.com/galaxyproject/galaxy/commit/0902c23f3491b4840b649a203315…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-14 (Thu, 14 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M test/qunit/tests/masthead_tests.js
Log Message:
-----------
Merge pull request #1501 from guerler/fix_disabled_000
[16.01] Fix disabled css
Compare: https://github.com/galaxyproject/galaxy/compare/2e62388b2f34...0902c23f3491
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: 55677f2d3db723c023540b8d640563a9f3ca04c5
https://github.com/galaxyproject/galaxy/commit/55677f2d3db723c023540b8d6405…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M test/unit/jobs/test_command_factory.py
Log Message:
-----------
Fix to ensure integrity of tool_script.sh also.
Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected.
Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable.
Commit: 2e62388b2f34ad83f215bb3eff4c6ae5b1efd7b7
https://github.com/galaxyproject/galaxy/commit/2e62388b2f34ad83f215bb3eff4c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-01-14 (Thu, 14 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M test/unit/jobs/test_command_factory.py
Log Message:
-----------
Merge pull request #1494 from jmchilton/tool_command_integrity
[16.01] Fix to ensure integrity of tool_script.sh also.
Compare: https://github.com/galaxyproject/galaxy/compare/9d52a4a31dd9...2e62388b2f34
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: 37f8038d63f8243151e817e9d564f90c58772c1f
https://github.com/galaxyproject/galaxy/commit/37f8038d63f8243151e817e9d564…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.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/layout/menu.js
Log Message:
-----------
Undo user icon in masthead
Commit: 9d52a4a31dd9e660855bf1e12bd07d3c49b73fd9
https://github.com/galaxyproject/galaxy/commit/9d52a4a31dd9e660855bf1e12bd0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.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/layout/menu.js
Log Message:
-----------
Merge pull request #1493 from guerler/undo_user_000
[16.01] Undo user icon in masthead
Compare: https://github.com/galaxyproject/galaxy/compare/becffe93a3f7...9d52a4a31dd9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e14449e62dbf89e2c4f8a41448582f332aaefdcf
https://github.com/galaxyproject/galaxy/commit/e14449e62dbf89e2c4f8a4144858…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view.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-parameters.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Revise label handling in form
Commit: 84fd89d67a5a9cca9647cdf6dedd86fe7786cb44
https://github.com/galaxyproject/galaxy/commit/84fd89d67a5a9cca9647cdf6dedd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-01-13 (Wed, 13 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view.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-parameters.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge pull request #1496 from guerler/labels_000
Revise label handling in form
Compare: https://github.com/galaxyproject/galaxy/compare/91fe9d09aab5...84fd89d67a5a
Branch: refs/heads/dev
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: 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.
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.
Commit: e13fb12569a84c78b23b71e0f90bcea13439bc53
https://github.com/galaxyproject/galaxy/commit/e13fb12569a84c78b23b71e0f90b…
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:
-----------
Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0
Commit: 91fe9d09aab5e78115ba87c42406b709796119dc
https://github.com/galaxyproject/galaxy/commit/91fe9d09aab5e78115ba87c42406…
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:
-----------
Merge pull request #1497 from jmchilton/dev_merge_0
Merge 16.01 into dev.
Compare: https://github.com/galaxyproject/galaxy/compare/790953e6e786...91fe9d09aab5