Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f7ffde9db447be807f3c7924bbfe243c3f6faa51
https://github.com/galaxyproject/galaxy/commit/f7ffde9db447be807f3c7924bbfe…
Author: Dannon Baker <dannon.baker(a)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/db444455b29b008b0f3bdf0844f3…
Author: Dannon Baker <dannon.baker(a)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/074ec18490e2fb86c17a506374d7…
Author: Dannon Baker <dannon.baker(a)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/69c74d52d4a4614aa544abd2c7a8…
Author: Dannon Baker <dannon.baker(a)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/2ad4dde0729bbce690f744730b4b…
Author: Dannon Baker <dannon.baker(a)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/46290939092a8068836712176ddb…
Author: Dannon Baker <dannon.baker(a)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/7e220205f38abbe6d44f93f5ccfb…
Author: Dannon Baker <dannon.baker(a)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/cf3ed04d742938de52c24386dcf2…
Author: Dannon Baker <dannon.baker(a)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/6cf4c8e5f4780421dc45472bf495…
Author: Dannon Baker <dannon.baker(a)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/77dff21bcc6c1b2f93d400307a7f…
Author: Dannon Baker <dannon.baker(a)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/361b48a4d22e0f61ac6dcdf0d306…
Author: Dannon Baker <dannon.baker(a)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/9fe40db5b3cf82f09ae3a783a8b7…
Author: Dannon Baker <dannon.baker(a)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/0e39cf1924cfacb879802934da01…
Author: Dannon Baker <dannon.baker(a)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/18ae4457a131948fe87b7038215e…
Author: Dannon Baker <dannon.baker(a)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/f35c1d6630961f6ae5e9393ebd15…
Author: Dannon Baker <dannon.baker(a)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/87dc52cd8fedf64e895d0aa84212…
Author: Dannon Baker <dannon.baker(a)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/5a0f98802cab73dfcdaef01b1200…
Author: Nicola Soranzo <nicola.soranzo(a)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/ed56454ca07f3e07ce2bfced8614…
Author: Martin Cech <marten(a)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/36fcb5c1b74f7b7b848273111339…
Author: Martin Cech <marten(a)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/753ecd625c1410a3a6dc2c4a30e3…
Author: mvdbeek <m.vandenbeek(a)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/12f51a47897faf55461626a504b6…
Author: Nicola Soranzo <nicola.soranzo(a)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/f1adf0a7920720ea7f20cdc3a21e…
Author: Martin Cech <marten(a)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/75c9610fdaf1a59806e75458e04f…
Author: Martin Cech <marten(a)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/20cf8b5bf0f4632d0f3c275c3261…
Author: Martin Cech <marten(a)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/54ec854c130f92f49d2c3f42e2e8…
Author: Martin Cech <marten(a)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/85265ebd793a43d8df048e613cdf…
Author: Martin Cech <marten(a)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/a56c4e9cf6b929e43dd2dcb6891b…
Author: Martin Cech <marten(a)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/7eb927b631a3677a74b055fc275b…
Author: John Chilton <jmchilton(a)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/7cc01380afd017c5cac2af2b2d73….
Commit: 9957c027375c436b64299240982a2165d83b7ff3
https://github.com/galaxyproject/galaxy/commit/9957c027375c436b64299240982a…
Author: John Chilton <jmchilton(a)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/3c36bec2903e6c012428912c424f…
Author: Sebastian Kapust <sebastian(a)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/96fbe9702dc07eb965a6e6ede3db…
Author: Martin Cech <marten(a)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/dba21dc8a42640b679d1076bb7f8…
Author: John Chilton <jmchilton(a)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/e7b7bee82e60acea478db2dbf2cc…
Author: Nate Coraor <nate(a)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/99c1da2f62739654d72a598908ea…
Author: Nicola Soranzo <nicola.soranzo(a)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
Compare: https://github.com/galaxyproject/galaxy/compare/44275a2b722f...99c1da2f6273
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 5a0f98802cab73dfcdaef01b1200e96bc6b9a8ae
https://github.com/galaxyproject/galaxy/commit/5a0f98802cab73dfcdaef01b1200…
Author: Nicola Soranzo <nicola.soranzo(a)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: e7b7bee82e60acea478db2dbf2cc03552ebf6cd4
https://github.com/galaxyproject/galaxy/commit/e7b7bee82e60acea478db2dbf2cc…
Author: Nate Coraor <nate(a)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
Compare: https://github.com/galaxyproject/galaxy/compare/dba21dc8a426...e7b7bee82e60
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4b99dca85cd277e12fd8213d6abdf6e283fe4fb6
https://github.com/galaxyproject/galaxy/commit/4b99dca85cd277e12fd8213d6abd…
Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Fix default job script by moving env setup
The part where pythonpath was evaluated totally ignored any variables set in the env setup. That is now fixed. All credits go to @mvdbeek for finding the cause of the issue and proposing the solution.
Commit: bbce9a1e6f1a077dfbbb795f643f5578b40436f2
https://github.com/galaxyproject/galaxy/commit/bbce9a1e6f1a077dfbbb795f643f…
Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Change location of env setup
Commit: 77cd1fc30a6beabc3cde7ae22e1f62dd2560b94c
https://github.com/galaxyproject/galaxy/commit/77cd1fc30a6beabc3cde7ae22e1f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-10 (Sun, 10 Jun 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Need to set default HOME/TMP before env_setup_commands
Otherwise the defaults take precedence
Commit: 7f2117b26b531edc52b564f7435503c6072a233c
https://github.com/galaxyproject/galaxy/commit/7f2117b26b531edc52b564f74355…
Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Merge pull request #1 from mvdbeek/rhpvorderman-patch-1
Need to set default HOME/TMP before env_setup_commands
Commit: 47c03ab2514d833225b41ff0c67f3652aa4c6b22
https://github.com/galaxyproject/galaxy/commit/47c03ab2514d833225b41ff0c67f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Merge pull request #6305 from rhpvorderman/patch-1
Fix default job script by moving env setup
Compare: https://github.com/galaxyproject/galaxy/compare/ada8a7f6fb78...47c03ab2514d
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 57f319531e9c05c6a30dc8f6ffbe507831dbc7c6
https://github.com/galaxyproject/galaxy/commit/57f319531e9c05c6a30dc8f6ffbe…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-06-06 (Wed, 06 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
To clear workflow tool search field press ESC or click the X button
Commit: c78d7ef5131ee807660e032f865a355459c0dfb0
https://github.com/galaxyproject/galaxy/commit/c78d7ef5131ee807660e032f865a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Missing semicolon.
Commit: 544cc610fd07376c961ab3b4a38d1c6b28eeb6ad
https://github.com/galaxyproject/galaxy/commit/544cc610fd07376c961ab3b4a38d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/list-item.scss
Log Message:
-----------
Client format
Commit: 1df5959d216a812e344716c94cd836649da042ee
https://github.com/galaxyproject/galaxy/commit/1df5959d216a812e344716c94cd8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/list-item.scss
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge branch 'workflow.tool.search.clear' into dev
Commit: ada8a7f6fb78c53f54cd3dc3c156fd8476c2840f
https://github.com/galaxyproject/galaxy/commit/ada8a7f6fb78c53f54cd3dc3c156…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Client format (from the merge)
Compare: https://github.com/galaxyproject/galaxy/compare/e61a05ebf467...ada8a7f6fb78
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1825ea53c981e7cf3d0206e63a534e3f288b90b8
https://github.com/galaxyproject/galaxy/commit/1825ea53c981e7cf3d0206e63a53…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/app.py
Log Message:
-----------
Put import at the top
Commit: 178a94ad2a8bce2fe80372fb1790b903683fddd3
https://github.com/galaxyproject/galaxy/commit/178a94ad2a8bce2fe80372fb1790…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Move `get_mercurial_default_options_dict()` where it's used
Commit: 6c56467641d6eea97aaefd5bf8370f06665bb03f
https://github.com/galaxyproject/galaxy/commit/6c56467641d6eea97aaefd5bf837…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Use Mercurial CLI instead of API for `commit_changeset()`
Commit: 1831dbe3f30fe18a5bef7e51034494cc7f70f3ee
https://github.com/galaxyproject/galaxy/commit/1831dbe3f30fe18a5bef7e510344…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Use Mercurial CLI instead of API for `add_changeset()`
Commit: bd31c3e7b63a7d2f7266f1b964c566c87c100cc2
https://github.com/galaxyproject/galaxy/commit/bd31c3e7b63a7d2f7266f1b964c5…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Use Mercurial CLI instead of API for `pull_repository()`
Merge `get_configured_ui()` into `get_repo_for_repository()`.
Commit: 0ca83cbc7c7e10023e3e967b08510c7d7e83cf94
https://github.com/galaxyproject/galaxy/commit/0ca83cbc7c7e10023e3e967b0851…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Use Mercurial CLI instead of API for `remove_file()`
Commit: fa78aeab876faac14d1c1ee9ff80c59dd7c6d839
https://github.com/galaxyproject/galaxy/commit/fa78aeab876faac14d1c1ee9ff80…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Remove unnecessary calls to `get_repo_for_repository()`
Commit: bba60a05359f4c19e53dd3360402076a0e399e74
https://github.com/galaxyproject/galaxy/commit/bba60a05359f4c19e53dd3360402…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Use `hg init` to create a Mercurial repository
This allows removing a call to `hg_util.get_repo_for_repository()`, which
uses the discouraged Mercurial API.
Commit: 7c75c230bf7b4ff0c132a814b50f10cc8c31671b
https://github.com/galaxyproject/galaxy/commit/7c75c230bf7b4ff0c132a814b50f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Remove unused functions
Commit: 42999955f74388ef639464879f48c08f92985657
https://github.com/galaxyproject/galaxy/commit/42999955f74388ef639464879f48…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Use `hg id` to map a changeset to a revision number
This allows removing a lot of calls to `hg_util.get_repo_for_repository()`,
which uses the discouraged Mercurial API.
Commit: db4c5a97eded69c6b76ced2bcada1801cad3bd85
https://github.com/galaxyproject/galaxy/commit/db4c5a97eded69c6b76ced2bcada…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Fix `reversed_upper_bounded_changelog()` calls
`hg_util.reversed_upper_bounded_changelog()` expects a changeset revision
string as second parameter, not a `changectx` object.
Commit: f270f7abfbe885b4d8dc198f100e26856a5cadec
https://github.com/galaxyproject/galaxy/commit/f270f7abfbe885b4d8dc198f100e…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Merge pull request #6307 from nsoranzo/mercurial_api_removal3
More use of Mercurial CLI instead of API
Compare: https://github.com/galaxyproject/galaxy/compare/9a798395d13a...f270f7abfbe8
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 1f6736fbf4a6335dcd79f24d2ed3c4bdb9bafbb1
https://github.com/galaxyproject/infrastructure-playbook/commit/1f6736fbf4a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
R env/jsiu/templates
A env/jsiu/templates/slurm/slurm.conf.j2
A env/jsiu/templates/supervisor
A roles/slurmscale/files/templates/slurm/slurm.conf.j2
R roles/slurmscale/files/templates/slurm/slurm.conf.j2
Log Message:
-----------
Move elastic slurm conf to jsiu env (eventually to jscommon)
Commit: 3a3c08bff7f8647add6b2823511c08f55581acc9
https://github.com/galaxyproject/infrastructure-playbook/commit/3a3c08bff7f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
R env/jsiu/instance_inventory
Log Message:
-----------
Remove old instance_inventory from prior elastic attempt
Commit: f495dd5166ed9fe19add6cd2f965f2b89000d052
https://github.com/galaxyproject/infrastructure-playbook/commit/f495dd5166e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M env/jsiu/group_vars/all.yml
M env/jsiu/group_vars/controllers/vars.yml
M env/jsiu/group_vars/cvmfsclients.yml
M env/jsiu/inventory
A env/jsiu/playbook.yml
R env/jsiu/playbook.yml
A roles/openstack/tasks/clean.yml
A roles/openstack/tasks/main.yml
A roles/openstack/tasks/secrets.yml
A roles/openstack/tasks/spawn.yml
M roles/slurmscale/files/group_vars/all/cluster.yml
A roles/slurmscale/files/library
M roles/slurmscale/tasks/main.yml
M roles/slurmscale/templates/group_vars/all/cloud.yml.j2
Log Message:
-----------
More slurmscale WIP, the controller is launchable from the playbook now
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1f3c6d7f6e…
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 7eb927b631a3677a74b055fc275b90827bcdff21
https://github.com/galaxyproject/galaxy/commit/7eb927b631a3677a74b055fc275b…
Author: John Chilton <jmchilton(a)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/7cc01380afd017c5cac2af2b2d73….
Commit: 9957c027375c436b64299240982a2165d83b7ff3
https://github.com/galaxyproject/galaxy/commit/9957c027375c436b64299240982a…
Author: John Chilton <jmchilton(a)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/3c36bec2903e6c012428912c424f…
Author: Sebastian Kapust <sebastian(a)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/96fbe9702dc07eb965a6e6ede3db…
Author: Martin Cech <marten(a)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/dba21dc8a42640b679d1076bb7f8…
Author: John Chilton <jmchilton(a)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
Compare: https://github.com/galaxyproject/galaxy/compare/a56c4e9cf6b9...dba21dc8a426
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.