Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8af5671953df12e5207a8b3e5e70c742cea9f158
https://github.com/galaxyproject/galaxy/commit/8af5671953df12e5207a8b3e5e70…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-13 (Sun, 13 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
M test/qunit/tests/workflow_editor_tests.js
M test/unit/tools/test_parameter_parsing.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Allow input collections to specify mutiple collection types.
Parallelling format specifier which can take multiple formats.
Commit: 5a441044fbc1b773f9a59f12050a8b7dcda11694
https://github.com/galaxyproject/galaxy/commit/5a441044fbc1b773f9a59f12050a…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
M test/qunit/tests/workflow_editor_tests.js
M test/unit/tools/test_parameter_parsing.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge pull request #1308 from jmchilton/multi_collection_types
Allow input collections to specify multiple collection types.
Compare: https://github.com/galaxyproject/galaxy/compare/4c0bb9902ada...5a441044fbc1
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168
https://github.com/galaxyproject/galaxy/commit/3924a5a0e3d2c7d787e81fabc4e2…
Author: Mark Iskander <motiontracker(a)gmail.com>
Date: 2015-12-07 (Mon, 07 Dec 2015)
Changed paths:
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Fixed indentation errors
Commit: 7b45f7b4047377dc1e5c622a3dc6449e3c68f9ad
https://github.com/galaxyproject/galaxy/commit/7b45f7b4047377dc1e5c622a3dc6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Merge pull request #1259 from markiskander/reporter_fixes
Fixed indentation errors for Reports
Compare: https://github.com/galaxyproject/galaxy/compare/5d26f589cc47...7b45f7b40473
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d24bc3df1e627a0586860600a89352f6bddf49b1
https://github.com/galaxyproject/galaxy/commit/d24bc3df1e627a0586860600a893…
Author: Lance Parsons <lparsons(a)genomics.princeton.edu>
Date: 2015-12-16 (Wed, 16 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
Log Message:
-----------
Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS
Commit: 1c21ba82417f2a6d3e8d024ccd3a60a3416f5340
https://github.com/galaxyproject/galaxy/commit/1c21ba82417f2a6d3e8d024ccd3a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
Log Message:
-----------
Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables.
Commit: 9bbe4b869e000e0b86e85e19743390c0bed77d57
https://github.com/galaxyproject/galaxy/commit/9bbe4b869e000e0b86e85e197433…
Author: Lance Parsons <lparsons(a)yahoo.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
Log Message:
-----------
Merge pull request #1 from natefoo/lparsons_galaxy_slots
Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables.
Commit: 4c0bb9902ada3ed2dea7f1eeeb047aa4f9228be0
https://github.com/galaxyproject/galaxy/commit/4c0bb9902ada3ed2dea7f1eeeb04…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
Log Message:
-----------
Merge pull request #1347 from lparsons/galaxy_slots
Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS
Compare: https://github.com/galaxyproject/galaxy/compare/28cf2822f7bb...4c0bb9902ada
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 61f4c82642c5f48057d36fb9c728b66242807879
https://github.com/galaxyproject/galaxy/commit/61f4c82642c5f48057d36fb9c728…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
A test/api/test_workflow_missing_tool.ga
M test/api/test_workflows.py
Log Message:
-----------
Add test case for importing a workflow with missing tool.
Commit: bed79b5e6a90965c0c0ba73a3c14851319ab90d2
https://github.com/galaxyproject/galaxy/commit/bed79b5e6a90965c0c0ba73a3c14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Fix importing pre-16.01 workflows with missing tools.
Fixes #1386 (thanks to @trevor for the bug report).
Test with:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_import_missing_tool
```
Commit: 28cf2822f7bb3497cedee1951c22ca21e3aca956
https://github.com/galaxyproject/galaxy/commit/28cf2822f7bb3497cedee1951c22…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
A test/api/test_workflow_missing_tool.ga
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #1416 from jmchilton/workflow_missing_tool_import
Fix importing pre-16.01 workflows with missing tools.
Compare: https://github.com/galaxyproject/galaxy/compare/607db31b0432...28cf2822f7bb
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 339ad57f3fa626fe30c1bf26f90e0647be038cc9
https://github.com/galaxyproject/galaxy/commit/339ad57f3fa626fe30c1bf26f90e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-12-30 (Wed, 30 Dec 2015)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/frame.less
R client/galaxy/style/less/masthead.less
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/templates/charts.mako
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/ui/ui-frames.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/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/onload.js
M static/style/blue/base.css
M static/style/blue/masthead.css
M templates/webapps/galaxy/galaxy.masthead.mako
Log Message:
-----------
Cleanup Masthead and Scratchbook
Cleanup Masthead and Scratchbook
Commit: 4cd621dd378e3a9db0d934203a5e1cdebd817b6c
https://github.com/galaxyproject/galaxy/commit/4cd621dd378e3a9db0d934203a5e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-12-31 (Thu, 31 Dec 2015)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.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/layout/scratchbook.js
A test/qunit/tests/masthead_tests.html
A test/qunit/tests/masthead_tests.js
Log Message:
-----------
Add test cases
Commit: 34bb21c411c3ebce94e67f996e70387d33e7f8cf
https://github.com/galaxyproject/galaxy/commit/34bb21c411c3ebce94e67f996e70…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/frame.less
R client/galaxy/style/less/masthead.less
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/templates/charts.mako
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/ui/ui-frames.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/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/onload.js
M static/style/blue/base.css
M static/style/blue/masthead.css
M templates/webapps/galaxy/galaxy.masthead.mako
A test/qunit/tests/masthead_tests.html
A test/qunit/tests/masthead_tests.js
Log Message:
-----------
Merge pull request #1407 from guerler/revise_masthead_000
Masthead/Scratchbook revision and test cases
Compare: https://github.com/galaxyproject/galaxy/compare/905adbac3899...34bb21c411c3
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a6cbb88ad12288eca031c0469113abc831a42d37
https://github.com/galaxyproject/galaxy/commit/a6cbb88ad12288eca031c0469113…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Enable tool isolation by default and fix bugs.
Commit: 1084f14dd0637bc47978a33122c74d86cb617241
https://github.com/galaxyproject/galaxy/commit/1084f14dd0637bc47978a33122c7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M test/unit/jobs/test_command_factory.py
Log Message:
-----------
Unit test modifications for running tool commands in isolated scripts.
Commit: 7f8e37d5a1aa96c2c839acea4511e071e81eb450
https://github.com/galaxyproject/galaxy/commit/7f8e37d5a1aa96c2c839acea4511…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Attempt to fix samtools resolution for metadata when tool command externalized.
Commit: acab90d63c6c96a6e609f32080f5b610b33dd549
https://github.com/galaxyproject/galaxy/commit/acab90d63c6c96a6e609f32080f5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Fix unicode-y problem with tool command externalization.
Commit: 340aef2550d16bb987b36bc7b2df8e0ed4f6f56b
https://github.com/galaxyproject/galaxy/commit/340aef2550d16bb987b36bc7b2df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-02 (Sat, 02 Jan 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Fix logging for tool script externalization.
Commit: 7cbf41feb3dfd6eb12c99630692776565c72c579
https://github.com/galaxyproject/galaxy/commit/7cbf41feb3dfd6eb12c996306927…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-03 (Sun, 03 Jan 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Better exception when samtools is required but not on PATH.
Commit: 905adbac38992ae2fc889d23f000fa2541e87939
https://github.com/galaxyproject/galaxy/commit/905adbac38992ae2fc889d23f000…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/util/__init__.py
M test/unit/jobs/test_command_factory.py
Log Message:
-----------
Merge pull request #1412 from jmchilton/isolate
Isolate tool commands by default.
Compare: https://github.com/galaxyproject/galaxy/compare/10677319f74f...905adbac3899