Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3a17db8f205f57902b35b2245c8367802beb5faa
https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things
Convert history-contents urlroot to instance var
remove outdated comment
Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7
https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Rebuild client w/ maps.
Commit: c2307f3f1aae8f46fd1023accdf0a6c1c435eba3
https://github.com/galaxyproject/galaxy/commit/c2307f3f1aae8f46fd1023accdf0…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
added missing level fatal_oom to xsd
Commit: 8d75a67386f72814c17ad1abef5d0154b247a521
https://github.com/galaxyproject/galaxy/commit/8d75a67386f72814c17ad1abef5d…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
also added missing documentation
Commit: fc47618f6798d48f3ab903a8ea6231067bf0fed2
https://github.com/galaxyproject/galaxy/commit/fc47618f6798d48f3ab903a8ea62…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
A scripts/plugin_staging.py
Log Message:
-----------
Initial python-based plugin staging. to be used from common startup.
Commit: e110489cc55f25b7d5ec7b9e5cbc5d914215b806
https://github.com/galaxyproject/galaxy/commit/e110489cc55f25b7d5ec7b9e5cbc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently)
Commit: 9ac0161891a92db7a359e13a74e831ec17a79317
https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Update description for installing pbs-python
Commit: 370ea25d2c58b7e55f6bc062062e9a962a08ea7d
https://github.com/galaxyproject/galaxy/commit/370ea25d2c58b7e55f6bc062062e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M scripts/plugin_staging.py
Log Message:
-----------
Minor refactoring, comments.
Commit: 8364ebebcd81b6f8bf6c1122e5271a5c5eb23868
https://github.com/galaxyproject/galaxy/commit/8364ebebcd81b6f8bf6c1122e527…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M scripts/get_uwsgi_args.py
Log Message:
-----------
Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink
Commit: 4cdd210bb27cd1c271e69c8dfd46585f0c232ef9
https://github.com/galaxyproject/galaxy/commit/4cdd210bb27cd1c271e69c8dfd46…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M scripts/plugin_staging.py
Log Message:
-----------
Use os.pardir instead of ../. Thanks @nsoranzo
Commit: 37ad1a8bdce963b4152331685e3755a60777e633
https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Merge pull request #6345 from mvdbeek/update_pbs_python_doc
[18.01] Update description for installing pbs-python
Commit: cddee94e4bb043381433030e34f3f9129382830f
https://github.com/galaxyproject/galaxy/commit/cddee94e4bb043381433030e34f3…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Small fixes
Commit: 12a05c782099da0eb846069fe96355fb50212fef
https://github.com/galaxyproject/galaxy/commit/12a05c782099da0eb846069fe963…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M scripts/common_startup.sh
M scripts/get_uwsgi_args.py
A scripts/plugin_staging.py
Log Message:
-----------
Merge pull request #6344 from dannon/python_static_staging
[18.05] Visualization static staging
Commit: a2ff5efbce3023b12a774600b331867d7320898a
https://github.com/galaxyproject/galaxy/commit/a2ff5efbce3023b12a774600b331…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-16 (Sat, 16 Jun 2018)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd
[18.05] Added missing level fatal_oom to xsd
Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f
https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Merge pull request #6336 from dannon/backport_url_fix_flattened
[18.01] Backport backbone url fixes (flattened)
Commit: e8beea0d60c1a4b88b67cc3f176e11ae76215f67
https://github.com/galaxyproject/galaxy/commit/e8beea0d60c1a4b88b67cc3f176e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: 6e02c9aff7650f6dad05ff18683ac19b10648ee4
https://github.com/galaxyproject/galaxy/commit/6e02c9aff7650f6dad05ff18683a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
M lib/galaxy/tools/xsd/galaxy.xsd
M scripts/common_startup.sh
M scripts/get_uwsgi_args.py
A scripts/plugin_staging.py
Log Message:
-----------
Merge branch 'release_18.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/02974b79c7a9...6e02c9aff765
**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: 3a17db8f205f57902b35b2245c8367802beb5faa
https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things
Convert history-contents urlroot to instance var
remove outdated comment
Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7
https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Rebuild client w/ maps.
Commit: 9ac0161891a92db7a359e13a74e831ec17a79317
https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Update description for installing pbs-python
Commit: 37ad1a8bdce963b4152331685e3755a60777e633
https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Merge pull request #6345 from mvdbeek/update_pbs_python_doc
[18.01] Update description for installing pbs-python
Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f
https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Merge pull request #6336 from dannon/backport_url_fix_flattened
[18.01] Backport backbone url fixes (flattened)
Commit: e8beea0d60c1a4b88b67cc3f176e11ae76215f67
https://github.com/galaxyproject/galaxy/commit/e8beea0d60c1a4b88b67cc3f176e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M doc/source/admin/cluster.md
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Compare: https://github.com/galaxyproject/galaxy/compare/a2ff5efbce30...e8beea0d60c1
**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_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 3a17db8f205f57902b35b2245c8367802beb5faa
https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things
Convert history-contents urlroot to instance var
remove outdated comment
Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7
https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Rebuild client w/ maps.
Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f
https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
Merge pull request #6336 from dannon/backport_url_fix_flattened
[18.01] Backport backbone url fixes (flattened)
Compare: https://github.com/galaxyproject/galaxy/compare/37ad1a8bdce9...3707fb4eb128
**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: 7c8ac3ed7209d6076dad937ef0e390d7b95c0fa8
https://github.com/galaxyproject/galaxy/commit/7c8ac3ed7209d6076dad937ef0e3…
Author: Mataivic <victor.mataigne(a)wanadoo.fr>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Add a condition to FilterFailedDatasetsTool to remove empty files
Hello,
Here is an extra-condition for the tool ``FilterFailedDatasetsTool`` to allow it to remove empty datasets as well as failed datasets in a collection. I tested it on my data and it seems to work fine. Since it's my first time looking at galaxy's source code, I don't know if there is a proper way to do that ... And I didn't make the improvement for paired datasets because I don't have proper data to test it. But I assume it would be something like ``if forward_o.is_ok and reverse_o.is_ok and forward_o.has_data() and reverse_o.has_data():`` ?
Commit: b27281aaedbf0dc26c8d577d20168e8592bdfc9c
https://github.com/galaxyproject/galaxy/commit/b27281aaedbf0dc26c8d577d2016…
Author: Mataivic <victor.mataigne(a)wanadoo.fr>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
improved filtering of empty files in a collection (1)
- Supplemental parameter : 'remove_empty' which allow the user to choose if he/she wants to keep or not empty files in the collection.
- Coming next : the modified wrapper.
(Edited directly on GitHub).
Commit: f4ec64a0057c81a62baf3874e3ac726f89fa86ac
https://github.com/galaxyproject/galaxy/commit/f4ec64a0057c81a62baf3874e3ac…
Author: Mataivic <victor.mataigne(a)wanadoo.fr>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
modified wrapper filter_failed_collection
- Supplemental 'select' parameter : 'remove_empty'
Commit: 7c87dfdffda17b2cc6878e3a7dba9da9a70da45b
https://github.com/galaxyproject/galaxy/commit/7c87dfdffda17b2cc6878e3a7dba…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Simplify and modularize FilterFailedDatasetsTool class
Commit: 8a4d18fba160aed43e15d2852093d6f8ded96dc9
https://github.com/galaxyproject/galaxy/commit/8a4d18fba160aed43e15d2852093…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_empty_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add filter empty collection tool
I think having a separate tool for this task makes sense and makes the
distinction between empty and fialed datasets clearer.
Commit: babe2e5cc58502d9d0ba33fbd1ec0caf7a1c2b56
https://github.com/galaxyproject/galaxy/commit/babe2e5cc58502d9d0ba33fbd1ec…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Change get_new_elements to _get_new_elements
And use same order for arguments in signature and caller.
Commit: 46d8b318baac455ac3ff4c5782cfd9f6718e55bc
https://github.com/galaxyproject/galaxy/commit/46d8b318baac455ac3ff4c5782cf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Correct help text of filter_failed_collection and filter_empty_collection tools
Commit: 0507818bbe3c712b506045458702122293780741
https://github.com/galaxyproject/galaxy/commit/0507818bbe3c712b506045458702…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Add tests for filtering list:pair and list:list:pair collections
Commit: 5992629619a39408f9e8a3082de96f1d73592f7c
https://github.com/galaxyproject/galaxy/commit/5992629619a39408f9e8a3082de9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Map over list or list:paired collection in filter collection tools
Commit: 72dd53f55e7ae8ad3a18278da88cc800d7f6572e
https://github.com/galaxyproject/galaxy/commit/72dd53f55e7ae8ad3a18278da88c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-13 (Wed, 13 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update comments to the fact that we're processing list or list:paired collections
Commit: 02974b79c7a9d9cbe45b8ad08d7a532c11fcbe0b
https://github.com/galaxyproject/galaxy/commit/02974b79c7a9d9cbe45b8ad08d7a…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-06-17 (Sun, 17 Jun 2018)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
M test/api/test_tools.py
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #5640 from Mataivic/patch-1
Add a FilterEmptyDatasetsTool and allow filtering tools to apply to arbitrary collection structures
Compare: https://github.com/galaxyproject/galaxy/compare/db11a2549d33...02974b79c7a9
**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.