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https://github.com/galaxyproject/galaxy
06 April 2024, 09:42:01 UTC
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Revision Author Date Message Commit Date
fdb1804 John Chilton 26 February 2019, 19:28:25 UTC Update version to 19.01 26 February 2019, 19:28:25 UTC
7553326 John Chilton 26 February 2019, 19:23:03 UTC Merge pull request #7415 from dannon/fix-workflow-drop-hack [19.01] Fix workflow list drop-to-upload 26 February 2019, 19:23:03 UTC
1583eec Dannon Baker 26 February 2019, 16:14:36 UTC Client formatting sync for 19.01 26 February 2019, 16:14:36 UTC
14f3ce3 Dannon Baker 26 February 2019, 16:12:22 UTC Fix workflow interface drop to import 26 February 2019, 16:12:22 UTC
bd25ff9 Martin Cech 26 February 2019, 15:40:01 UTC Merge pull request #7414 from mvdbeek/fix_analyze_75 [19.01] Fix analyze 75 datatype upload 26 February 2019, 15:40:01 UTC
ed37599 mvdbeek 26 February 2019, 11:22:46 UTC Fix analyze75 hdr file upload when convert newlines is on 26 February 2019, 11:22:46 UTC
47ed81f mvdbeek 26 February 2019, 11:06:02 UTC Remove unreachable print statement I don't think an exception could ever occur here. 26 February 2019, 11:06:07 UTC
808aa5b Nate Coraor 22 February 2019, 18:23:16 UTC Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 22 February 2019, 18:23:16 UTC
9b72f5a Nicola Soranzo 22 February 2019, 18:16:25 UTC Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments [18.09] Update configuration samples 22 February 2019, 18:16:25 UTC
8651e1e John Chilton 22 February 2019, 18:12:16 UTC Merge branch 'release_18.09' into release_19.01 22 February 2019, 18:12:16 UTC
2f973ac John Chilton 22 February 2019, 18:11:49 UTC Merge branch 'release_18.05' into release_18.09 22 February 2019, 18:11:49 UTC
1529758 John Chilton 22 February 2019, 18:11:19 UTC Merge branch 'release_18.01' into release_18.05 22 February 2019, 18:11:19 UTC
656b3c2 John Chilton 04 December 2018, 15:37:57 UTC Refactor dataset fetching in get/set dataset method in web controller. 22 February 2019, 18:10:12 UTC
5fc5b4a Marius van den Beek 22 February 2019, 16:41:24 UTC Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions 22 February 2019, 16:41:24 UTC
a83eb67 Nate Coraor 22 February 2019, 16:31:44 UTC Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. 22 February 2019, 16:31:44 UTC
351c188 Nicola Soranzo 22 February 2019, 12:07:16 UTC Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports 22 February 2019, 12:07:16 UTC
1a0f067 Martin Cech 21 February 2019, 17:26:31 UTC change config schema to reflect removing paste options 21 February 2019, 17:26:31 UTC
4ad4fe5 Martin Cech 21 February 2019, 16:57:49 UTC Merge pull request #7399 from dannon/bump_yarn_network_tolerance [19.01] Bump yarn network tolerance 21 February 2019, 16:57:49 UTC
726ad9a Dannon Baker 21 February 2019, 16:48:11 UTC Bump yarn's network timeout from 2 minutes to 5 minutes. 21 February 2019, 16:48:11 UTC
8c9c27b mvdbeek 21 February 2019, 16:45:56 UTC Drop filter-with from docs / .sample 21 February 2019, 16:45:56 UTC
648d016 Martin Cech 20 February 2019, 17:12:27 UTC Merge pull request #7390 from mvdbeek/more_useful_error_message [19.01] Report line number mismatch in sort collection tool 20 February 2019, 17:12:27 UTC
015ce5c Martin Cech 20 February 2019, 16:52:47 UTC Merge pull request #7308 from jmchilton/19.01_release_notes [19.01] Release notes for 19.01. 20 February 2019, 16:52:47 UTC
b4fc7c1 mvdbeek 20 February 2019, 12:52:03 UTC Report line number mismatch in sort collection tool Otherwise this would just fail because sorted_elements is undefined. I don't think there can be a HDA without metadata, so I've dropped that check. 20 February 2019, 12:53:26 UTC
ac9b300 Martin Cech 19 February 2019, 15:55:16 UTC Merge pull request #7385 from blankenberg/19.01-anvio-datatypes [19.01] Add datatypes for Anvi'o 19 February 2019, 15:55:16 UTC
6d24026 Marius van den Beek 19 February 2019, 15:42:06 UTC Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments remove Paste config option, reword URL prefix 19 February 2019, 15:42:06 UTC
d72f82d Martin Cech 19 February 2019, 15:37:34 UTC remove Paste config option, reword URL prefix 19 February 2019, 15:37:34 UTC
35529a0 Björn Grüning 19 February 2019, 12:28:58 UTC Merge pull request #7384 from jmchilton/fix_h5_assertion_docs [19.01] Fix HDF5 test assert docs 19 February 2019, 12:28:58 UTC
737bae8 Nicola Soranzo 19 February 2019, 00:43:12 UTC Reword HDF5 attribute test docs 19 February 2019, 00:43:12 UTC
51280fb Daniel Blankenberg 18 February 2019, 20:26:31 UTC flip a line 18 February 2019, 20:26:31 UTC
cf31e33 Daniel Blankenberg 18 February 2019, 19:25:19 UTC Decrease readability. 18 February 2019, 19:25:19 UTC
948cdb2 Daniel Blankenberg 18 February 2019, 18:53:03 UTC cleanup anvio.py 18 February 2019, 18:53:03 UTC
7abd448 Daniel Blankenberg 18 February 2019, 18:48:13 UTC Add datatypes for Anvi'o 18 February 2019, 18:48:13 UTC
2033535 John Chilton 18 February 2019, 18:05:07 UTC Fix HDF5 test assert docs Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements. 18 February 2019, 18:09:12 UTC
37a9397 Nicola Soranzo 18 February 2019, 13:36:45 UTC Fix PR link 18 February 2019, 13:36:45 UTC
ca4acf7 Nicola Soranzo 18 February 2019, 13:29:42 UTC Sort PR numbers Small fixes. 18 February 2019, 13:29:42 UTC
94bcb8d John Chilton 18 February 2019, 13:01:50 UTC More fixes to 19.01 release notes. 18 February 2019, 13:01:50 UTC
2a3555d John Chilton 18 February 2019, 12:51:45 UTC Better Singularity summary thanks to @mvdbeek. 18 February 2019, 12:52:09 UTC
072b8d7 Marius van den Beek 18 February 2019, 12:47:35 UTC Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton@gmail.com> 18 February 2019, 12:47:35 UTC
16af734 Marius van den Beek 18 February 2019, 12:47:28 UTC Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton@gmail.com> 18 February 2019, 12:47:28 UTC
b67dc2b Dannon 14 February 2019, 21:56:14 UTC Merge pull request #7353 from bgruening/improve_err_message Improve error message during tool testing 14 February 2019, 21:56:14 UTC
728ff20 John Chilton 14 February 2019, 18:57:44 UTC Merge pull request #7352 from bgruening/test_data_fix fix the filename of saved test-data 14 February 2019, 18:57:44 UTC
45d06ac John Chilton 13 February 2019, 22:40:20 UTC Merge pull request #7354 from dannon/comm_server_fixes [19.01] Communication Server Display Fixes 13 February 2019, 22:40:20 UTC
62d8d80 John Chilton 13 February 2019, 19:25:41 UTC Merge pull request #7331 from mvdbeek/test_data_managers [19.01] Discriminate data managers and allow managed testing 13 February 2019, 19:25:41 UTC
b29b8b5 Dannon Baker 12 February 2019, 19:27:49 UTC Use standard bootstrap classes for sizing here since it's only used in one spot. 12 February 2019, 21:43:05 UTC
bfeb272 Dannon Baker 12 February 2019, 19:18:44 UTC drop redundant communication server frame styles. 12 February 2019, 21:43:05 UTC
f320850 Dannon Baker 12 February 2019, 19:18:01 UTC Drop 'fade in' classes on iframe; prefer static display without extra animations and fixes opacity issue from biostar. 12 February 2019, 21:43:05 UTC
f311ebd Bjoern Gruening 12 February 2019, 21:28:32 UTC mention planemo explicitly 12 February 2019, 21:28:32 UTC
740fc85 Bjoern Gruening 12 February 2019, 21:22:43 UTC improve test error message 12 February 2019, 21:22:43 UTC
06d1e5a Bjoern Gruening 12 February 2019, 20:12:02 UTC fix the name of presevered test-data 12 February 2019, 20:12:02 UTC
b33b064 Nicola Soranzo 12 February 2019, 11:51:07 UTC Merge branch 'release_18.09' into release_19.01 12 February 2019, 11:51:07 UTC
9c9c8a5 Martin Cech 12 February 2019, 02:28:46 UTC Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version 12 February 2019, 02:28:46 UTC
f7322d8 Björn Grüning 09 February 2019, 13:42:28 UTC Merge pull request #7299 from chambm/feature/rawtar-datatypes Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs 09 February 2019, 13:42:28 UTC
f002696 Nate Coraor 07 February 2019, 23:23:04 UTC Merge pull request #7309 from erasche/more-contrast [19.01] More contrast in CSS 07 February 2019, 23:23:04 UTC
d710bb8 mvdbeek 07 February 2019, 11:02:31 UTC Discriminate data managers and allow managed testing I am not a big fan of the heuristic in which we fall back to loading the data manager tool relative to the data_manager_conf.xml file, but I don't really see a better way here. 07 February 2019, 22:35:02 UTC
8f7263a John Chilton 07 February 2019, 19:49:33 UTC Merge pull request #7301 from bgruening/hdf5_tests Add new test syntax specific for HDF5 files 07 February 2019, 19:49:33 UTC
23d4af5 Helena Rasche 06 February 2019, 18:25:38 UTC Revert "Add box-shadow" This reverts commit 87c82595771438b0e8244b32885430e4fe1bab6e. 06 February 2019, 18:25:38 UTC
e3f1234 Martin Cech 06 February 2019, 17:14:44 UTC Merge pull request #7310 from erasche/fix-emoji-tags [19.01] Fix emoji tags 06 February 2019, 17:14:44 UTC
dd91709 Marius van den Beek 06 February 2019, 15:04:13 UTC Only block the single category of C characters that is problematic Co-Authored-By: erasche <hxr@hx42.org> 06 February 2019, 15:40:40 UTC
b59d76e Helena Rasche 05 February 2019, 23:40:54 UTC Fix emoji tags 06 February 2019, 15:40:40 UTC
d36cf51 Bjoern Gruening 06 February 2019, 15:31:15 UTC change "name" to "key" 06 February 2019, 15:31:15 UTC
dc303f0 Matt Chambers 06 February 2019, 15:18:57 UTC Remove try/except in sniffers Add .d/.raw to file_ext 06 February 2019, 15:18:57 UTC
12fde52 Helena Rasche 06 February 2019, 15:18:32 UTC remove inaccurate comment 06 February 2019, 15:18:32 UTC
87c8259 Helena Rasche 06 February 2019, 15:18:14 UTC Add box-shadow 06 February 2019, 15:18:14 UTC
0a7583b Helena Rasche 05 February 2019, 22:24:01 UTC More contrast 06 February 2019, 14:52:08 UTC
b5713ca John Chilton 05 February 2019, 19:50:13 UTC Progress on 19.01 release notes... 05 February 2019, 20:47:11 UTC
d30852b Matt Chambers 05 February 2019, 18:14:06 UTC Add wiff.tar extension and sniffer 05 February 2019, 18:14:06 UTC
c4fbe94 Nicola Soranzo 05 February 2019, 17:37:27 UTC Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step [19.01] Don't reduce list:list in multi data input workflow step 05 February 2019, 17:37:27 UTC
413af14 Matt Chambers 05 February 2019, 17:00:31 UTC Fix lint errors 05 February 2019, 17:00:31 UTC
365ac40 Matt Chambers 05 February 2019, 16:52:11 UTC Fix lint errors 05 February 2019, 16:52:11 UTC
3d4ff4f Björn Grüning 05 February 2019, 15:19:35 UTC Merge pull request #41 from jmchilton/hdf5_tests Tweaks to hdf5 testing. 05 February 2019, 15:19:35 UTC
a36b56e mvdbeek 05 February 2019, 14:39:35 UTC Drop redundant wait for history wait_for_invocation_and_jobs does that already, thx @nsoranzo. 05 February 2019, 14:39:42 UTC
ae8bf6f John Chilton 05 February 2019, 14:35:07 UTC Release notes raw. 05 February 2019, 14:35:07 UTC
2a97f72 John Chilton 05 February 2019, 13:45:46 UTC Tweaks to hdf5 testing. - This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions. 05 February 2019, 13:45:46 UTC
cf68cbe mvdbeek 05 February 2019, 11:37:40 UTC Verify that list:list will be reduced to list in multi data input 05 February 2019, 13:11:27 UTC
4df1de3 mvdbeek 04 February 2019, 22:46:25 UTC Map over multiple=true in workflow run There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior). 05 February 2019, 13:11:27 UTC
e9f40f2 Bjoern Gruening 05 February 2019, 03:24:57 UTC fix pep8 05 February 2019, 03:24:57 UTC
cb13e56 Bjoern Gruening 05 February 2019, 03:23:13 UTC add test-data for new hdf5 based tool test 05 February 2019, 03:23:13 UTC
a00fd50 Bjoern Gruening 05 February 2019, 03:22:46 UTC adopt XSD for new syntax 05 February 2019, 03:22:46 UTC
d4420b7 Bjoern Gruening 05 February 2019, 03:22:15 UTC register new test tool 05 February 2019, 03:22:15 UTC
db2987b Bjoern Gruening 05 February 2019, 03:21:02 UTC add test tool for new assertions 05 February 2019, 03:21:02 UTC
e37036a Bjoern Gruening 05 February 2019, 03:20:28 UTC add hdf5 assert tests 05 February 2019, 03:20:28 UTC
d79514b Bjoern Gruening 05 February 2019, 03:19:53 UTC allow assertions on binary inputs 05 February 2019, 03:19:53 UTC
68a66f4 Bjoern Gruening 05 February 2019, 03:18:49 UTC update h5py dependency 05 February 2019, 03:18:49 UTC
9f501bb Matt Chambers 04 February 2019, 20:26:40 UTC Add datatypes and sniffers for several directory-based mass spectrometry formats: Bruker BAF, Agilent/Bruker YEP, Bruker TDF, Agilent MassHunter, and Waters MassLynx 04 February 2019, 20:26:40 UTC
526bebb Martin Cech 04 February 2019, 19:46:05 UTC Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01 [19.01] Remove errant space in intermine_simple_display.loc.sample 04 February 2019, 19:46:05 UTC
428c663 Daniel Blankenberg 04 February 2019, 19:32:02 UTC Remove errant space in intermine_simple_display.loc.sample 04 February 2019, 19:32:02 UTC
49cbad5 Daniel Blankenberg 02 February 2019, 15:02:07 UTC Merge pull request #7191 from natefoo/admin-docs-19.01 [19.01] Properly document handler assignment method configuration and fix logging configuration docs 02 February 2019, 15:02:07 UTC
74fcf12 Nate Coraor 02 February 2019, 02:46:20 UTC Incorporate suggestions from @nsoranzo 02 February 2019, 02:47:48 UTC
9a133e9 Nicola Soranzo 02 February 2019, 02:34:04 UTC Remove spurious characters Co-Authored-By: natefoo <nate@bx.psu.edu> 02 February 2019, 02:34:04 UTC
038d1a1 Helena Rasche 01 February 2019, 20:00:33 UTC Revert "Darker tool form in workflow editor" This reverts commit bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479. 01 February 2019, 20:00:33 UTC
bdc6243 Helena Rasche 01 February 2019, 19:59:51 UTC Darker tool form in workflow editor 01 February 2019, 19:59:51 UTC
6cdca79 John Chilton 31 January 2019, 01:01:47 UTC Merge pull request #7277 from mvdbeek/fix_install_via_tool_id [19.01] Fix installing tools via tool_id 31 January 2019, 01:01:47 UTC
152e001 Nicola Soranzo 29 January 2019, 15:50:39 UTC Merge branch 'release_18.09' into release_19.01 29 January 2019, 15:50:39 UTC
c8b3d5e Marius van den Beek 29 January 2019, 14:29:22 UTC Merge pull request #7275 from jmchilton/1901_migrate_tools [18.09] Stop tool migrations checking by default... 29 January 2019, 14:29:22 UTC
7061f2a mvdbeek 28 January 2019, 18:52:46 UTC Fix installing tools via tool_id 28 January 2019, 18:53:36 UTC
d83db6a John Chilton 27 January 2019, 20:48:16 UTC Stop with tool migrations by default, they are not needed in modern Galaxies... ... and even problematic in some ways. 27 January 2019, 20:48:16 UTC
8c93a91 Nicola Soranzo 24 January 2019, 20:19:13 UTC Merge pull request #7267 from dannon/toolshed-roup-detail-view-typo [19.01] Fix _.escape typo in toolshed group detail view 24 January 2019, 20:19:13 UTC
12128ad Dannon Baker 24 January 2019, 18:37:24 UTC Fix _.escape typo in toolshed group detail view 24 January 2019, 18:37:24 UTC
dc6ec1e Dannon Baker 24 January 2019, 18:19:59 UTC Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 24 January 2019, 18:19:59 UTC
6a660e9 Dannon 24 January 2019, 18:19:27 UTC Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid [18.09] Fix install operation in installed_repository_grid 24 January 2019, 18:19:27 UTC
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