https://github.com/galaxyproject/galaxy

sort by:
Revision Author Date Message Commit Date
868acc3 Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 21 January 2016, 17:24:27 UTC
aad5d9a Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). 21 January 2016, 17:04:23 UTC
c13b1c0 Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. 08 January 2016, 20:17:38 UTC
90bed00 Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js 08 January 2016, 15:14:52 UTC
7b45f7b Merge pull request #1259 from markiskander/reporter_fixes Fixed indentation errors for Reports 04 January 2016, 20:37:43 UTC
5d26f58 Merge pull request #1295 from jmchilton/test_fixes_backport_15_10 [15.10] Backport various testing fixes. 22 December 2015, 18:19:01 UTC
52b66d0 Merge pull request #1385 from martenson/port-marius-ts-fix [15.10] Port marius TS fix 22 December 2015, 18:04:09 UTC
c3580da Allow installation of different repositories with the same name in a single install transaction. 22 December 2015, 17:16:25 UTC
2817eab Fail maxseconds test tool if sleep is interrupted. 18 December 2015, 13:25:49 UTC
57a7606 Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. 18 December 2015, 13:25:48 UTC
641b275 Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. 18 December 2015, 13:25:48 UTC
ffb9734 Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. 18 December 2015, 13:25:48 UTC
93c6d05 Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. 18 December 2015, 13:25:48 UTC
f042fe8 Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.test_libraries/LibrariesApiTestCase/test_create_dataset/ - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. 18 December 2015, 13:25:48 UTC
abd51e7 Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association 17 December 2015, 19:31:17 UTC
2d7c201 Merge pull request #1360 from martenson/raise-specific-exception [15.10] datalibs: raise and show specific exception and warning when no files detected 17 December 2015, 19:01:18 UTC
b4683fb raise and show specific exception and warning when no files detected 17 December 2015, 17:40:09 UTC
b0deead Fix change handler association 17 December 2015, 16:40:25 UTC
1b3ee81 Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. 16 December 2015, 15:22:23 UTC
a23e644 Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process 15 December 2015, 18:12:20 UTC
31f174a Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. 15 December 2015, 17:20:42 UTC
c48965f Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. 15 December 2015, 15:49:09 UTC
f953005 Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. 15 December 2015, 14:51:09 UTC
11eca70 When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. 14 December 2015, 18:06:27 UTC
9b30b13 Reduce code duplication by reusing get_installed_repository() function. 14 December 2015, 18:06:27 UTC
989f961 Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. 12 December 2015, 01:45:35 UTC
66146ad Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns 11 December 2015, 22:08:17 UTC
760c2b5 Properly show and label hidden datasets on rerurn 11 December 2015, 19:57:59 UTC
6a47d2d Merge pull request #1239 from jmchilton/collection_outputs_hidden [15.10] "Fix" collection outputs to hide the HDAs in the history. 10 December 2015, 23:57:24 UTC
fba354c Merge pull request #1282 from natefoo/kombu-el-cap [15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection 10 December 2015, 20:25:02 UTC
f13e929 Merge pull request #1278 from nsoranzo/release_15.10_config [15.10] Log a warning for missing tool whitelist file only if explicitly defined. 10 December 2015, 20:16:45 UTC
2835aea Merge pull request #2 from dannon/release_15.10_config Adjustments to sanitize_whitelist reloading. 10 December 2015, 20:05:55 UTC
b6e7b9a Adjustments to sanitize_whitelist reloading. 10 December 2015, 19:50:37 UTC
a9034b5 Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection. 09 December 2015, 20:54:55 UTC
0d98cf8 Log a warning for missing tool whitelist file only if explicitly defined. Also fix the log message. 09 December 2015, 18:23:27 UTC
2be1707 Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. 08 December 2015, 13:36:46 UTC
94b0499 Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% 08 December 2015, 12:25:41 UTC
3924a5a Fixed indentation errors 07 December 2015, 21:44:13 UTC
41a56ea Fix list collection creator being cutoff by restoring height: 100% 07 December 2015, 20:55:17 UTC
7d4eac1 Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. 05 December 2015, 23:10:01 UTC
e186b6a Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. 04 December 2015, 22:42:33 UTC
f34d701 Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. 04 December 2015, 21:06:47 UTC
736bf3c Merge pull request #1234 from natefoo/pulsar-missing-param [15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner 04 December 2015, 18:11:19 UTC
107de0e Add the missing "amqp_ack_republish_time" param for the Pulsar runner (it's available in the Pulsar client lib). 04 December 2015, 16:35:42 UTC
f08d518 Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. 04 December 2015, 15:32:47 UTC
7923360 "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files 04 December 2015, 15:26:40 UTC
8334593 Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. 03 December 2015, 22:00:54 UTC
516b079 Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. 03 December 2015, 21:36:25 UTC
d1684e7 Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 03 December 2015, 21:13:51 UTC
2b697e3 Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . 03 December 2015, 20:05:50 UTC
c9abc2b Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . 03 December 2015, 20:00:22 UTC
2c0ad43 Use test param label instead of param label in conditional upgrade missing message. 03 December 2015, 17:30:34 UTC
6c9a82e Fix for Section upgrade messages. 03 December 2015, 17:27:01 UTC
d83e8d3 Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section 03 December 2015, 16:38:55 UTC
ee5a87a Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. 03 December 2015, 16:33:27 UTC
a5b7e6c Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). 03 December 2015, 15:48:30 UTC
30b13bb Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment 02 December 2015, 20:32:05 UTC
c04b3a5 Re-add egg imports 02 December 2015, 14:26:36 UTC
51cd41b Fix ScIdx sniff method to handle first line comment 02 December 2015, 14:24:04 UTC
da2cc58 Merge pull request #1194 from martenson/release_15.10 [15.10] docs - deprecate TS direct hg api 30 November 2015, 19:39:17 UTC
5bd8981 deprecate TS direct hg api 30 November 2015, 19:35:45 UTC
a03404c Merge pull request #1162 from martenson/fix-datalibs [15.10] Fix two bugs in datalibs 30 November 2015, 18:57:15 UTC
c532f68 Merge pull request #1186 from gregvonkuster/release_15.10 [15.10] Add support for Strand-specific Coordinate Count datatype 30 November 2015, 18:56:24 UTC
21fad8a Set the column names and edit the comments section 30 November 2015, 12:48:08 UTC
6fdff2d Add Strand-specific Coordinate Count datatype entry to the datatypes config. 28 November 2015, 19:32:12 UTC
87b9d1a Add support for Strand-specific COordinate Count datatype 28 November 2015, 19:28:38 UTC
a5200a4 Merge pull request #1172 from martenson/fix-dockerimage-version [15.10] run 15.10 tests on older docker image 25 November 2015, 17:33:44 UTC
be7b003 try running 15.10 on older docker image 25 November 2015, 16:14:50 UTC
d89670e Merge pull request #1170 from martenson/fix-password-reset [15.10] fix missing configuration which broke TS password reset 25 November 2015, 16:06:00 UTC
aa52b6c add pretty_datetime_format to TS config sample 25 November 2015, 15:56:04 UTC
7a4be88 fix missing configuration; broke TS password reset 25 November 2015, 14:53:11 UTC
e19b7f6 fix the extra slash in URL when creating folder 23 November 2015, 20:14:15 UTC
39bc057 fix whitespace 23 November 2015, 20:12:05 UTC
e142bea replace wrong class name 23 November 2015, 20:08:25 UTC
95507c5 fix whitespace 23 November 2015, 20:07:40 UTC
82ce624 Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. 23 November 2015, 14:52:40 UTC
286f714 Merge pull request #1085 from guerler/fix_grids_000 [15.10] Fix dataset grid history change 20 November 2015, 18:08:26 UTC
09db120 Merge pull request #1141 from martenson/tweak-notes [15.10] release notes tweaks 20 November 2015, 17:46:38 UTC
ceb8ee1 Merge pull request #11 from dannon/tweak-notes Slight wording tweak 20 November 2015, 17:03:44 UTC
a5aeea0 Slight wording tweak 20 November 2015, 16:56:27 UTC
e9ed5bf clarify the bitbucket support 20 November 2015, 16:45:58 UTC
a98e56c Merge pull request #868 from jmchilton/release_notes [15.10] Release notes 20 November 2015, 16:24:03 UTC
76fc6be add text highlights 20 November 2015, 15:30:04 UTC
cf16e2c add bitbucker deprecation notice 20 November 2015, 15:27:59 UTC
743603b Merge pull request #1140 from dannon/menufix_2 [15.10] Don't override search url 20 November 2015, 15:14:12 UTC
adcf513 Simply remove tool_search_url -- it isn't used and it's totally composable. 20 November 2015, 14:47:01 UTC
cbf5c68 Don't override search url -- this currently affects main where Help->Search ends up at root.com... 20 November 2015, 14:44:01 UTC
ed992b3 A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). 20 November 2015, 02:03:30 UTC
0fdca7d A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). 20 November 2015, 01:27:25 UTC
eb16ba3 Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. 18 November 2015, 17:51:00 UTC
05f3da3 Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` 18 November 2015, 12:25:38 UTC
73f46f4 Merge branch 'release_15.07' into release_15.10 18 November 2015, 10:06:53 UTC
27dc31a Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). 17 November 2015, 20:14:59 UTC
05e6682 Merge pull request #1112 from nsoranzo/release_15.10_data_libraries_beta [15.10] Deprecate old library UI in the "Shared Data" menu. 17 November 2015, 20:14:13 UTC
e61e30c Merge pull request #1100 from martenson/fix-ts-api-install [15.10] Fix API installation of tool_dependencies 17 November 2015, 20:11:51 UTC
3ffa607 Deprecate old library UI in the "Shared Data" menu. 17 November 2015, 17:24:39 UTC
040118a Encode unicode string before passing to hashlib.sha1(). Fixes #673. 16 November 2015, 19:58:56 UTC
937f99b Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d4488437ffef9e5acf So I think this should be part of 15.10. Thanks to Greg for fixing this one. 16 November 2015, 03:28:18 UTC
7150983 Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. 15 November 2015, 04:25:27 UTC
75e7e4c Fix 500 error when attempting to update installed repository. 14 November 2015, 22:09:21 UTC
back to top