| 0182d8d | Martin Cech | 13 March 2018, 15:45:07 UTC | Update version to 18.01 | 13 March 2018, 15:45:07 UTC |
| 31cb24e | Martin Cech | 13 March 2018, 15:39:10 UTC | add built client with maps for 18.01 tagging | 13 March 2018, 15:39:10 UTC |
| 040bf5b | Martin Cech | 13 March 2018, 15:04:10 UTC | Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs | 13 March 2018, 15:04:10 UTC |
| 5cf3d44 | Dannon Baker | 13 March 2018, 14:53:24 UTC | Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax | 13 March 2018, 14:53:24 UTC |
| 8dfc152 | Dannon Baker | 13 March 2018, 12:04:17 UTC | Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job | 13 March 2018, 12:04:17 UTC |
| f1dd060 | mvdbeek | 13 March 2018, 11:38:41 UTC | Test rename PJA when resuming a failed job | 13 March 2018, 11:38:41 UTC |
| 6a7fb23 | Dannon Baker | 13 March 2018, 11:26:01 UTC | Instead of denoting unused var from items(), just use values() | 13 March 2018, 11:26:01 UTC |
| b685b53 | Dannon Baker | 12 March 2018, 20:51:29 UTC | Ship context along with PJA execution when remapping workflow immediate actions | 12 March 2018, 20:51:29 UTC |
| 1a5f6a3 | Martin Cech | 12 March 2018, 20:38:45 UTC | Merge pull request #5677 from natefoo/docker-swarm-race [18.01] Additional error handling for GIE container launching | 12 March 2018, 20:38:45 UTC |
| 04404f9 | Dannon Baker | 12 March 2018, 19:58:17 UTC | Support re-execution of immediate PJAs when requing jobs | 12 March 2018, 19:58:17 UTC |
| 6b9afb6 | Martin Cech | 12 March 2018, 19:28:51 UTC | rmeove overly zealous syntax fix thanks to dannon | 12 March 2018, 19:28:51 UTC |
| 332d79e | Dannon Baker | 12 March 2018, 18:50:33 UTC | Fix 'uknown' typo in model exceptions | 12 March 2018, 18:50:33 UTC |
| cb5e81b | Martin Cech | 12 March 2018, 18:37:22 UTC | replace incorrect list add syntax | 12 March 2018, 18:37:22 UTC |
| 4fea390 | Martin Cech | 12 March 2018, 18:15:32 UTC | Merge pull request #5674 from jmchilton/unsorted_bam_rename [18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. | 12 March 2018, 18:15:32 UTC |
| d632b41 | Nate Coraor | 12 March 2018, 17:03:17 UTC | Fix GIE launch for cases when the published port isn't available immediately (seems to happen with Swarm Mode occasionally) | 12 March 2018, 17:03:17 UTC |
| 9c0c8ee | John Chilton | 12 March 2018, 16:47:01 UTC | Mention self.current_pr in release notes. | 12 March 2018, 16:47:18 UTC |
| 2db95b4 | John Chilton | 12 March 2018, 14:35:29 UTC | Rename datatype extension 'bam_native' to 'unsorted.bam'. We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do. | 12 March 2018, 16:29:57 UTC |
| 513b6a5 | Dannon Baker | 19 December 2017, 15:14:16 UTC | Fix a few mutable default params in workflow/run_request. | 12 March 2018, 15:55:48 UTC |
| cf4936b | Dannon Baker | 19 December 2017, 13:52:23 UTC | Minor cleanup in galaxy.tools.actions | 12 March 2018, 15:55:04 UTC |
| 83fa18d | Nate Coraor | 12 March 2018, 15:34:18 UTC | Display error message on IE template fill exception | 12 March 2018, 15:54:01 UTC |
| c034ab3 | Nate Coraor | 12 March 2018, 15:47:52 UTC | Merge pull request #5668 from martenson/18.01_release_notes [18.01] Release Notes | 12 March 2018, 15:47:52 UTC |
| df03a59 | Martin Cech | 09 March 2018, 21:57:08 UTC | move some sections deeper in the document to make the highlights more focused | 09 March 2018, 21:57:08 UTC |
| c5ead79 | Nicola Soranzo | 09 March 2018, 12:22:59 UTC | Add #5643 to release notes | 09 March 2018, 12:22:59 UTC |
| e72e02c | Nicola Soranzo | 09 March 2018, 12:08:14 UTC | Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. | 09 March 2018, 12:08:14 UTC |
| 235d6c3 | Nicola Soranzo | 09 March 2018, 11:58:27 UTC | Condense some entries | 09 March 2018, 11:58:27 UTC |
| 804f815 | Nicola Soranzo | 09 March 2018, 11:43:28 UTC | Fix bullet list indentation | 09 March 2018, 11:43:28 UTC |
| e68ac4a | Nicola Soranzo | 09 March 2018, 11:39:04 UTC | Highlights fixes | 09 March 2018, 11:39:04 UTC |
| 9e27427 | John Chilton | 09 March 2018, 03:33:21 UTC | Small language tweaks. Including fixes from :eagle::eyes:. | 09 March 2018, 03:33:21 UTC |
| 6d4b839 | John Chilton | 09 March 2018, 03:30:46 UTC | Spell check 18.01 release notes and small tweaks. | 09 March 2018, 03:30:46 UTC |
| b964722 | John Chilton | 09 March 2018, 03:20:13 UTC | More release 18.01 release note tweaks. | 09 March 2018, 03:20:23 UTC |
| 1923786 | John Chilton | 09 March 2018, 03:02:06 UTC | Condense many 18.01 release bullets, expand a few - part 3 of 1003. | 09 March 2018, 03:02:06 UTC |
| 1a68096 | John Chilton | 09 March 2018, 01:53:24 UTC | Condense many 18.01 release bullets, expand a few - part 2 of 1003. | 09 March 2018, 01:53:24 UTC |
| cb477dd | John Chilton | 09 March 2018, 01:35:24 UTC | Condense many 18.01 release bullets, expand a few. | 09 March 2018, 01:35:24 UTC |
| e923c61 | John Chilton | 09 March 2018, 01:24:43 UTC | More progress on release notes, still very rough. | 09 March 2018, 01:24:43 UTC |
| 3515d60 | John Chilton | 08 March 2018, 22:29:48 UTC | Another couple sentences of release docs. | 08 March 2018, 22:29:48 UTC |
| 02bf18f | John Chilton | 08 March 2018, 22:06:04 UTC | Some initial work on release highlights, still completely broken. | 08 March 2018, 22:07:17 UTC |
| 63292de | Martin Cech | 08 March 2018, 20:56:04 UTC | add trackster fix to RN | 08 March 2018, 20:56:04 UTC |
| fa3ec5f | John Chilton | 08 March 2018, 20:53:29 UTC | Merge pull request #5261 from dannon/trackster_fixes [18.01] Trackster fixes. | 08 March 2018, 20:53:29 UTC |
| 0229bf5 | Martin Cech | 08 March 2018, 19:41:02 UTC | announce removal of planttribe datatypes | 08 March 2018, 19:41:02 UTC |
| 9c9c69c | Martin Cech | 08 March 2018, 19:07:51 UTC | iniital work on RN | 08 March 2018, 19:07:51 UTC |
| 1761d85 | Martin Cech | 08 March 2018, 17:33:52 UTC | Merge pull request #5664 from mvdbeek/show_error_message_if_no_history_associated [18.01] Show error message if user tries purging datasets | 08 March 2018, 17:33:52 UTC |
| a0fd630 | Martin Cech | 08 March 2018, 17:17:28 UTC | Merge pull request #5665 from mvdbeek/show_error_msg_when_history_structure_cannot_be_shown [18.01] Show error message if history structure can't be shown | 08 March 2018, 17:17:28 UTC |
| 0a95f20 | Martin Cech | 08 March 2018, 17:16:34 UTC | Merge pull request #5663 from mvdbeek/user_activation_fix [18.01] Fix exception if email is not specified or email is wrong | 08 March 2018, 17:16:34 UTC |
| 3ce1273 | Martin Cech | 08 March 2018, 17:15:34 UTC | Merge pull request #5662 from mvdbeek/fix_build_filters [18.01] Fix exception if user preference value undefined | 08 March 2018, 17:15:34 UTC |
| fe444ab | mvdbeek | 08 March 2018, 14:19:35 UTC | Show error message if history structure can't be shown Fixes: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 494, in display_structured assert (history.user and (history.user.id == trans.user.id) or ``` | 08 March 2018, 15:21:21 UTC |
| 17e1786 | mvdbeek | 08 March 2018, 14:02:00 UTC | Avoid exception if email is wrong Avoids: ``` AttributeError: 'NoneType' object has no attribute 'active' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/user.py", line 938, in activate if user.active is True: ``` | 08 March 2018, 14:03:31 UTC |
| d60b80a | mvdbeek | 08 March 2018, 13:04:42 UTC | Show error message if user tries purging datasets without having an associated history. This can be seen by pasting http://<gx_instance>/history/purge_deleted_datasets into an anonymous browser session (be careful to not delete something important ;)). Traceback is: ``` AttributeError: 'NoneType' object has no attribute 'datasets' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 1108, in purge_deleted_datasets for hda in trans.history.datasets: ``` | 08 March 2018, 13:20:44 UTC |
| 706efdc | mvdbeek | 08 March 2018, 12:37:45 UTC | Fix exception if email is not specified We render a regular error a few lines lower. | 08 March 2018, 12:37:48 UTC |
| cdae689 | mvdbeek | 08 March 2018, 12:02:43 UTC | Fix exception if user preference value undefined Fixes the following traceback on main: ``` AttributeError: 'NoneType' object has no attribute 'strip' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/root.py", line 110, in index config.update(self._get_extended_config(trans)) File "galaxy/webapps/galaxy/controllers/root.py", line 57, in _get_extended_config 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), File "galaxy/tools/toolbox/base.py", line 963, in to_dict filter_method = self._build_filter_method(trans) File "galaxy/tools/toolbox/base.py", line 1004, in _build_filter_method filters = self._filter_factory.build_filters(trans) File "galaxy/tools/toolbox/filters/__init__.py", line 37, in build_filters if value.strip(): ``` | 08 March 2018, 12:02:46 UTC |
| 206182e | Björn Grüning | 08 March 2018, 09:13:51 UTC | Merge pull request #5650 from mvdbeek/missing_index_file_fixes [18.01] Use sample file path when adding missing indexes | 08 March 2018, 09:13:51 UTC |
| b601bcc | Dannon Baker | 07 March 2018, 20:00:08 UTC | Merge pull request #5659 from martenson/merge-in-17.09 [18.01] Merge with 17.09 | 07 March 2018, 20:00:08 UTC |
| b655a49 | Martin Cech | 07 March 2018, 18:43:03 UTC | re-add erroneously removed line | 07 March 2018, 18:43:50 UTC |
| 10f8c3b | Martin Cech | 07 March 2018, 17:47:59 UTC | Merge branch 'release_17.09' into release_18.01 dropped all static content from merge except of styles | 07 March 2018, 17:47:59 UTC |
| 2846fa0 | mvdbeek | 07 March 2018, 12:37:22 UTC | Use target file path when adding missing indexes Previously we would load a TS tool during installation and ask if any of its tool datat tables are missing loc files. If thats the case we copy the sample file and call `handle_found_index_file` for the particular missing *.loc path of this data table. This does not work if the data table already existed (e.g for built-in data tables), but was missing the *.loc file, since we would atempt to load that path. Instead we do now load the path to the loc file that we just copied. Should fix https://github.com/galaxyproject/galaxy/issues/5648. | 07 March 2018, 13:07:03 UTC |
| 9e6f3f5 | John Chilton | 07 March 2018, 00:23:30 UTC | Merge pull request #5644 from mvdbeek/disable_sniffer_qname_input_sorted [18.01] Do not sniff BamInputSorted | 07 March 2018, 00:23:30 UTC |
| 90b700b | mvdbeek | 06 March 2018, 19:09:45 UTC | Do not sniff BamInputSorted Only aligners should produce this datatype. If an alignment is not explicitly coordinate or queryname sorted it should be BamNative. Also addresses https://github.com/galaxyproject/galaxy/pull/5628#issuecomment-370874329, though I think the sniff order should be dependent on the order with which datatypes are loaded. | 06 March 2018, 19:10:25 UTC |
| f33eee1 | Dannon Baker | 06 March 2018, 19:02:46 UTC | Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods. | 06 March 2018, 19:02:46 UTC |
| 4bca4a0 | Dannon Baker | 06 March 2018, 18:44:30 UTC | Config.js fixes; it was trying to import itself and not use it. | 06 March 2018, 18:44:30 UTC |
| 2270f72 | John Chilton | 06 March 2018, 18:23:49 UTC | Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. | 06 March 2018, 18:26:47 UTC |
| 4850ca5 | Nicola Soranzo | 06 March 2018, 09:44:31 UTC | Merge pull request #5620 from jmchilton/conda_fixes_1801 [18.01] Conda fix for commands using stdout redirection. | 06 March 2018, 09:44:31 UTC |
| f8d44c2 | Marius van den Beek | 06 March 2018, 09:13:40 UTC | Merge pull request #5631 from martenson/genomespace [17.09] Changed GenomeSpace token handling to use manual OpenID association only | 06 March 2018, 09:13:40 UTC |
| f0df326 | Dannon Baker | 05 March 2018, 22:44:55 UTC | Use static getters for default painter preferences, fix 'defailt' ironic typo. | 05 March 2018, 22:44:55 UTC |
| ff9bc84 | Nicola Soranzo | 05 March 2018, 18:58:03 UTC | Merge branch 'release_17.09' into release_18.01 | 05 March 2018, 18:58:03 UTC |
| ec8c926 | Dannon Baker | 05 March 2018, 17:46:52 UTC | Refactoring in feature painter draw. | 05 March 2018, 17:46:52 UTC |
| 28724ab | Dannon Baker | 05 March 2018, 15:15:39 UTC | Merge pull request #5639 from nsoranzo/release_17.09_backport_5043 [17.09] Backport of #5043 | 05 March 2018, 15:15:39 UTC |
| a6593d4 | Matthias Bernt | 20 November 2017, 13:23:16 UTC | python3 fix strings can not be written to byte mode file handlers. writing resulted in: TypeError: a bytes-like object is required, not 'str' Alternative would be to make string byte. | 05 March 2018, 12:43:43 UTC |
| d778452 | John Chilton | 05 March 2018, 03:10:48 UTC | Merge pull request #5635 from mvdbeek/fix_optional_output_discovery [18.01] Fix output discovery if dir doesn't exist | 05 March 2018, 03:10:48 UTC |
| da86785 | mvdbeek | 02 March 2018, 20:33:46 UTC | Drop optional="true" altogther | 02 March 2018, 20:33:46 UTC |
| 7ed81e1 | mvdbeek | 02 March 2018, 19:27:16 UTC | Move `optional` tag to the output data element Thx @nsoranzo! | 02 March 2018, 19:27:21 UTC |
| e01f9fa | Martin Cech | 02 March 2018, 19:16:27 UTC | Merge pull request #5634 from guerler/fix_async_grid_links [18.01] Remove href from grid sorting links | 02 March 2018, 19:16:27 UTC |
| 69bbcda | Martin Cech | 02 March 2018, 18:00:00 UTC | build client | 02 March 2018, 18:00:00 UTC |
| 10cf046 | Martin Cech | 02 March 2018, 17:58:44 UTC | replace syntax that is too new | 02 March 2018, 17:58:44 UTC |
| d21d7d9 | mvdbeek | 02 March 2018, 17:06:04 UTC | Fix output discovery when directory doesn't exist This broke in 8b76a5a698fd3bc13d4acc38194221def9ed5163. Checking if `directory` is a directory is what we had done previously. | 02 March 2018, 17:38:06 UTC |
| bd69278 | mvdbeek | 02 March 2018, 16:57:45 UTC | Add a testcase for optional output discovery This test correctly fails with: ``` galaxy.jobs.runners.local ERROR 2018-03-02 17:55:32,396 Job wrapper finish method failed Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 152, in queue_job self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1381, in finish 'primary': self.tool.collect_primary_datasets(out_data, self.get_tool_provided_job_metadata(), tool_working_directory, input_ext, input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1614, in collect_primary_datasets return output_collect.collect_primary_datasets(self, output, tool_provided_metadata, job_working_directory, input_ext, input_dbkey=input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 372, in collect_primary_datasets for discovered_file in discover_files(name, tool_provided_metadata, dataset_collectors, job_working_directory, outdata): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 490, in discover_files for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 507, in walk_over_file_collectors for match in walk_over_extra_files(extra_file_collector.directory, extra_file_collector, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 519, in walk_over_extra_files for filename in os.listdir(directory): OSError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp5Tz0m9/tmpfUHHl6/tmpVBcnfI/database/job_working_directory_LJioiW/000/2/working/i_do_not_exist' ``` | 02 March 2018, 17:38:06 UTC |
| 7ffabb1 | guerler | 02 March 2018, 17:26:26 UTC | Remove unused variable | 02 March 2018, 17:26:26 UTC |
| 7254d55 | guerler | 02 March 2018, 15:48:29 UTC | Remove href from grid sorting links | 02 March 2018, 15:48:29 UTC |
| 41910f8 | Martin Cech | 01 March 2018, 21:10:01 UTC | Merge pull request #5615 from martenson/distinct-elts [18.01] fix for cases where panel elements have to_dict with different signature | 01 March 2018, 21:10:01 UTC |
| 6b782ad | Nuwan Goonasekera | 01 March 2018, 15:48:05 UTC | Changed GenomeSpace token handling to use manual OpenID association only | 01 March 2018, 20:03:12 UTC |
| 77d085a | John Chilton | 01 March 2018, 19:40:14 UTC | Merge pull request #5589 from mvdbeek/samtools_queryname_and_input_order_datatypes [18.01] Add queryname sorted and input sorted datatypes | 01 March 2018, 19:40:14 UTC |
| b96fd2c | Martin Cech | 28 February 2018, 16:55:59 UTC | enable cache for tools that inherit from Tool | 01 March 2018, 19:27:41 UTC |
| 5406a71 | Martin Cech | 28 February 2018, 16:05:38 UTC | pass the toolbox obj to make sure cache is available | 01 March 2018, 19:27:36 UTC |
| d648e22 | Martin Cech | 27 February 2018, 19:29:04 UTC | fix for cases where panel elements have to_dict with different signature we want to only cache Tools anyways, so this fixes other possible bug where section/label etc would have same id as a Tool change the detection of Tool object to avoid circular import errors Also use cache for dictifying sections, we should gain more speed from that. | 01 March 2018, 19:27:29 UTC |
| 87c70d8 | Nicola Soranzo | 01 March 2018, 15:54:48 UTC | Merge branch 'release_17.09' into release_18.01 Conflicts: lib/galaxy/tools/__init__.py | 01 March 2018, 15:54:48 UTC |
| 2d132a4 | Nicola Soranzo | 01 March 2018, 15:47:30 UTC | Merge pull request #5626 from mvdbeek/limit_extract_dna_legacy_versions [17.09] Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring galaxy to be importable | 01 March 2018, 15:47:30 UTC |
| 3dec3bd | mvdbeek | 01 March 2018, 13:19:04 UTC | Move `Extract genomic DNA 1` to list of version galaxy lib tools | 01 March 2018, 13:19:04 UTC |
| 7c9c977 | Dannon Baker | 28 February 2018, 20:07:20 UTC | Misc cleanup while trying to debug nonexistent paint vars. | 28 February 2018, 20:07:20 UTC |
| 166fe7e | John Chilton | 28 February 2018, 13:45:45 UTC | Conda fixes for 18.01 - stdout redirection. Broken in #5397 I think. | 28 February 2018, 13:47:56 UTC |
| 0e6e468 | Dannon Baker | 27 February 2018, 17:43:46 UTC | Import fixes in main trackster.js | 27 February 2018, 17:43:46 UTC |
| a90c3a1 | John Chilton | 27 February 2018, 15:23:58 UTC | Merge pull request #5583 from martenson/backport-toolbox-cache [18.01] Backport toolbox cache | 27 February 2018, 15:23:58 UTC |
| 50cd159 | Martin Cech | 27 February 2018, 15:12:24 UTC | Merge pull request #5574 from jmchilton/optimize_count_query_1 [18.01] Optimize count query in grids (Part 1). | 27 February 2018, 15:12:24 UTC |
| d8585f6 | Martin Cech | 27 February 2018, 15:08:28 UTC | Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. | 27 February 2018, 15:08:28 UTC |
| c840778 | Martin Cech | 26 February 2018, 17:24:55 UTC | Merge pull request #5605 from dannon/migrate_fix [18.01] Fix migration 0137's downgrade | 26 February 2018, 17:24:55 UTC |
| e3ced2c | Dannon Baker | 26 February 2018, 16:07:39 UTC | Fix migration 0137's downgrade -- previously failed to select the correct column to drop | 26 February 2018, 16:07:39 UTC |
| 8a88cb9 | Martin Cech | 23 February 2018, 18:50:01 UTC | move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes | 26 February 2018, 15:47:26 UTC |
| fc52fe5 | Martin Cech | 22 February 2018, 22:04:29 UTC | Merge pull request #5588 from jmchilton/backport_packaging [18.01] Replace distutils.version with packaging.version | 22 February 2018, 22:04:29 UTC |
| bb19c7e | mvdbeek | 22 February 2018, 16:59:15 UTC | Add queryname sorted and input sorted datatypes The queryname sorted datatype (BamQuerynameSorted) ensures that the file is queryname ordered. The BamInputSorted datatype can be used to describe the output of aligners, which usually keep mate pairs adjacent. The BamInputSorted datatype allows using tools that require mates to be adjacent, without requiring an explicit sorting step. This can reduce the time and space required for duplicate marking tools, HiC tools and structural variant detection tools that require mates to be grouped together in an alignment file. The BamQuerynameSorted has a converter that works for all datatypes that can be consumed by samtools. There is no converter for BamInputSorted, since BamQuerynameSorted is valid input for tools requiring BamInputSorted input. I'm targeting 18.01 since I think it would be very unfortunate if we start annotating aligners with the very loose BamNative datatype, since this datatype does not make any promises about sort order at all. This closes https://github.com/galaxyproject/galaxy/issues/5497, goes a long way towards the problems mentioned in https://github.com/galaxyproject/galaxy/issues/5496 and would make https://github.com/galaxyproject/tools-iuc/pull/1732 and https://github.com/galaxyproject/tools-iuc/pull/1591 better | 22 February 2018, 18:59:55 UTC |
| ce3b40c | Marius van den Beek | 22 February 2018, 18:42:29 UTC | Merge pull request #5578 from jmchilton/opt_dyn_collect [18.01] Fix repeated fetching dataset permissions in dynamic output collection. | 22 February 2018, 18:42:29 UTC |
| 8806030 | Nicola Soranzo | 30 January 2018, 13:37:50 UTC | Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . | 22 February 2018, 16:32:44 UTC |
| d937273 | John Chilton | 22 February 2018, 15:04:19 UTC | Merge pull request #5573 from nsoranzo/release_18.01_fix_filesystem_library_uploads [18.01] Do not remove external path files during library uploads | 22 February 2018, 15:04:19 UTC |
| 8cc675e | Martin Cech | 22 February 2018, 02:08:10 UTC | Merge pull request #5576 from jmchilton/workflow_paginate [18.01] Paginate published workflows grid. | 22 February 2018, 02:08:10 UTC |
