Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7ffde9db447be807f3c7924bbfe243c3f6faa51 https://github.com/galaxyproject/galaxy/commit/f7ffde9db447be807f3c7924bbfe2... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css
Log Message: ----------- Alias btn-xs to btn-sm for thinks (like welcome) which may have been customized and rely on the previous styles.
Commit: db444455b29b008b0f3bdf0844f38a4db1e457ef https://github.com/galaxyproject/galaxy/commit/db444455b29b008b0f3bdf0844f38... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css
Log Message: ----------- Alias btn-default to btn-secondary for backwards compatibility.
Commit: 074ec18490e2fb86c17a506374d78269c29ae03f https://github.com/galaxyproject/galaxy/commit/074ec18490e2fb86c17a506374d78... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css
Log Message: ----------- Missed label->badge translations.
Commit: 69c74d52d4a4614aa544abd2c7a810fa817b7404 https://github.com/galaxyproject/galaxy/commit/69c74d52d4a4614aa544abd2c7a81... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css
Log Message: ----------- Drop sm-badge-pad completely (standard styles handle this now)
Commit: 2ad4dde0729bbce690f744730b4b2f2af39b1fef https://github.com/galaxyproject/galaxy/commit/2ad4dde0729bbce690f744730b4b2... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js
Log Message: ----------- Convert history-contents urlroot to instance var
Commit: 46290939092a8068836712176ddbfc7641f69ada https://github.com/galaxyproject/galaxy/commit/46290939092a8068836712176ddbf... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css
Log Message: ----------- Fix history list bottom border
Commit: 7e220205f38abbe6d44f93f5ccfb14506838118a https://github.com/galaxyproject/galaxy/commit/7e220205f38abbe6d44f93f5ccfb1... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/history.scss
Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey)
Commit: cf3ed04d742938de52c24386dcf2f0c10409df71 https://github.com/galaxyproject/galaxy/commit/cf3ed04d742938de52c24386dcf2f... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css
Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration
Commit: 6cf4c8e5f4780421dc45472bf495694dd49aaa47 https://github.com/galaxyproject/galaxy/commit/6cf4c8e5f4780421dc45472bf4956... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css
Log Message: ----------- Fix one more busted fade
Commit: 77dff21bcc6c1b2f93d400307a7f3332772f9943 https://github.com/galaxyproject/galaxy/commit/77dff21bcc6c1b2f93d400307a7f3... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css
Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button
Commit: 361b48a4d22e0f61ac6dcdf0d306d17d89b9d166 https://github.com/galaxyproject/galaxy/commit/361b48a4d22e0f61ac6dcdf0d306d... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako
Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes.
Commit: 9fe40db5b3cf82f09ae3a783a8b708e78239f27f https://github.com/galaxyproject/galaxy/commit/9fe40db5b3cf82f09ae3a783a8b70... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css
Log Message: ----------- Fix list panel control message margins.
Commit: 0e39cf1924cfacb879802934da0112470cba9a0e https://github.com/galaxyproject/galaxy/commit/0e39cf1924cfacb879802934da011... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/style/scss/upload.scss
Log Message: ----------- This is correct now
Commit: 18ae4457a131948fe87b7038215e81dec647e3db https://github.com/galaxyproject/galaxy/commit/18ae4457a131948fe87b7038215e8... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss
Log Message: ----------- Formatting for styles and a couple misc files
Commit: f35c1d6630961f6ae5e9393ebd1504831765bcf8 https://github.com/galaxyproject/galaxy/commit/f35c1d6630961f6ae5e9393ebd150... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-30 (Wed, 30 May 2018)
Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js
Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links.
Commit: 87dc52cd8fedf64e895d0aa8421207f52a390e01 https://github.com/galaxyproject/galaxy/commit/87dc52cd8fedf64e895d0aa842120... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths: M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- Only show 'switch to this history' when the person in question is the history owner.
Commit: 5a0f98802cab73dfcdaef01b1200e96bc6b9a8ae https://github.com/galaxyproject/galaxy/commit/5a0f98802cab73dfcdaef01b1200e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-06-06 (Wed, 06 Jun 2018)
Changed paths: M lib/galaxy/jobs/runners/slurm.py
Log Message: ----------- Strip a spurious Slurm warning from job stderr
Reason for the Slurm warning ----------------------------
The Linux kernel memory controller (responsible for the memory cgroup) may run out of cgroup subsystem state (CSS) IDs. When a cgroup is created it is assigned a CSS ID to manage its state. Upon removal of the cgroup the corresponding state information (e.g. cache entries) may still exist and therefore the CSS ID is still held. When multiple frequent short-lived jobs are run on a cluster node, the number of available CSS IDs becomes exhausted and creating a new memory cgroup results in a ENOSPC ("No space left on device"), which is reported by SLURM with the message "unable to add task[pid=<PID>] to memory cg '(null)'" (even if jobs run fine).
There is a bugfix for the kernel that releases the CSS ID upon cgroup destruction, but it appears to be only available after Linux 4.4. We use CentOS 7, which is based on Linux 3.10. The only temporary solutions is to reboot the affected cluster node.
Thanks to @tuxtobin for the detailed analysis above.
Reason for this patch ---------------------
Many tools rely on an empty stderr to determine if the job was successful, either because they were never updated to use `<stdio>`/`detect_errors`, or because the underlying tool returns a non-zero exit code when successful, e.g. `tranalign` from https://toolshed.g2.bx.psu.edu/view/devteam/emboss_5/832c20329690 . Even using a `<regex>` inside `<stdio>` would not work because the Slurm warning contains the word `error`.
Commit: ed56454ca07f3e07ce2bfced8614ca3dc560649a https://github.com/galaxyproject/galaxy/commit/ed56454ca07f3e07ce2bfced8614c... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths: M scripts/grt/grt.yml.sample
Log Message: ----------- add the canonical url to grt config
Commit: 36fcb5c1b74f7b7b84827311133957eb7249b277 https://github.com/galaxyproject/galaxy/commit/36fcb5c1b74f7b7b8482731113395... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths: M scripts/grt/grt.yml.sample
Log Message: ----------- Merge pull request #6301 from martenson/grt-config
[18.05] add the canonical url to grt config
Commit: 753ecd625c1410a3a6dc2c4a30e3f81fb71be29e https://github.com/galaxyproject/galaxy/commit/753ecd625c1410a3a6dc2c4a30e3f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M lib/galaxy/jobs/handler.py
Log Message: ----------- Increase sleep if encountering exception
Commit: 12f51a47897faf55461626a504b61fa2793777d6 https://github.com/galaxyproject/galaxy/commit/12f51a47897faf55461626a504b61... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M lib/galaxy/jobs/handler.py
Log Message: ----------- Merge pull request #6304 from mvdbeek/sleep_more
[18.05] Increase sleep if encountering (DB locking) exception
Commit: f1adf0a7920720ea7f20cdc3a21ea014f9ddd699 https://github.com/galaxyproject/galaxy/commit/f1adf0a7920720ea7f20cdc3a21ea... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako
Log Message: ----------- Merge pull request #6238 from dannon/1805stylefixes_rebased
[18.05] Various style fixes for history, toolshed, messages (backport)
Commit: 75c9610fdaf1a59806e75458e04f1319e95f5a40 https://github.com/galaxyproject/galaxy/commit/75c9610fdaf1a59806e75458e04f1... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js
Log Message: ----------- Merge pull request #6243 from dannon/workflow_submit_text_backport
[18.05] Backport of Workflow Execution Text Fixup
Commit: 20cf8b5bf0f4632d0f3c275c3261f920bbf76211 https://github.com/galaxyproject/galaxy/commit/20cf8b5bf0f4632d0f3c275c3261f... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css
Log Message: ----------- Merge pull request #6226 from dannon/minor_style_fixes
[18.05] Two minor aliases for (exterior) backwards compatibility, minor badge tweaks
Commit: 54ec854c130f92f49d2c3f42e2e8971d6676a79a https://github.com/galaxyproject/galaxy/commit/54ec854c130f92f49d2c3f42e2e89... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js
Log Message: ----------- remove outdated comment
Commit: 85265ebd793a43d8df048e613cdfb4578f4f6e18 https://github.com/galaxyproject/galaxy/commit/85265ebd793a43d8df048e613cdfb... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js
Log Message: ----------- Merge pull request #6237 from dannon/history_contents_multiview
[18.05] Fix history contents w/ proxy prefix (multiview error)
Commit: a56c4e9cf6b929e43dd2dcb6891bd54706e21025 https://github.com/galaxyproject/galaxy/commit/a56c4e9cf6b929e43dd2dcb6891bd... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- Merge pull request #6260 from dannon/history-view-fixes
[18.05] History view 'import' button display based on ownership.
Commit: 7eb927b631a3677a74b055fc275b90827bcdff21 https://github.com/galaxyproject/galaxy/commit/7eb927b631a3677a74b055fc275b9... Author: John Chilton jmchilton@gmail.com Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message: ----------- Fix delete "Collection Only" option in history menu.
Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d735....
Commit: 9957c027375c436b64299240982a2165d83b7ff3 https://github.com/galaxyproject/galaxy/commit/9957c027375c436b64299240982a2... Author: John Chilton jmchilton@gmail.com Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue
Log Message: ----------- Fix file type error in RuleCollectionBuilder.
Commit: 3c36bec2903e6c012428912c424f4ad762d1b96a https://github.com/galaxyproject/galaxy/commit/3c36bec2903e6c012428912c424f4... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M config/plugins/webhooks/demo/search/script.js
Log Message: ----------- Fix tool search overlay link
Commit: 96fbe9702dc07eb965a6e6ede3db8e9df91f8e19 https://github.com/galaxyproject/galaxy/commit/96fbe9702dc07eb965a6e6ede3db8... Author: Martin Cech marten@bx.psu.edu Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-composite.js
Log Message: ----------- backport and build client
Commit: dba21dc8a42640b679d1076bb7f8089028aa31fa https://github.com/galaxyproject/galaxy/commit/dba21dc8a42640b679d1076bb7f80... Author: John Chilton jmchilton@gmail.com Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/hdca-li-edit.js M config/plugins/webhooks/demo/search/script.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-composite.js
Log Message: ----------- Merge pull request #6311 from martenson/backport-and-build
[18.05] Backport and build client changes
Commit: e7b7bee82e60acea478db2dbf2cc03552ebf6cd4 https://github.com/galaxyproject/galaxy/commit/e7b7bee82e60acea478db2dbf2cc0... Author: Nate Coraor nate@bx.psu.edu Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths: M lib/galaxy/jobs/runners/slurm.py
Log Message: ----------- Merge pull request #6293 from nsoranzo/release_18.05_strip_slurm_warning
[18.05] Strip a spurious Slurm warning from job stderr
Commit: 99c1da2f62739654d72a598908ea07b7d2e699a7 https://github.com/galaxyproject/galaxy/commit/99c1da2f62739654d72a598908ea0... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/slurm.py M scripts/grt/grt.yml.sample M static/style/blue/base.css
Log Message: ----------- Merge branch 'release_18.05' into dev
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