| dbf6d3a | John Chilton | 27 January 2020, 14:36:57 UTC | Merge pull request #9234 from mvdbeek/mount_configs_rw [20.01] Mount job_working_directory/configs rw | 27 January 2020, 14:36:57 UTC |
| 2e1c5e4 | Björn Grüning | 25 January 2020, 22:45:44 UTC | Merge pull request #9267 from mvdbeek/mulled_build_image_name_fix [20.01] Fix suffix for single target mulled builds | 25 January 2020, 22:45:44 UTC |
| 4448286 | mvdbeek | 25 January 2020, 18:20:59 UTC | Fix suffix for single target builds Without this single target builds with explicit `iamge_build` would be called quay.io/biocontainers/<package><image_build>, which is not right. | 25 January 2020, 18:21:03 UTC |
| 6fbe8c9 | Nicola Soranzo | 24 January 2020, 17:06:46 UTC | Merge branch 'release_19.09' into release_20.01 | 24 January 2020, 17:08:02 UTC |
| 83bd848 | Nicola Soranzo | 24 January 2020, 17:03:20 UTC | Merge pull request #9266 from mvdbeek/fix_iteritems_in_workflow_extraction [19.09] Fix iteritems use in build_from_current_history.mako | 24 January 2020, 17:03:20 UTC |
| 6bb6aa2 | Marius van den Beek | 24 January 2020, 15:59:13 UTC | Merge pull request #9263 from nsoranzo/release_19.09_backport_9260 [19.09] Backport #9260 plus refactor | 24 January 2020, 15:59:13 UTC |
| f405dbf | mvdbeek | 24 January 2020, 14:24:44 UTC | Fix iteritems use in build_from_current_history.mako Fixes https://github.com/galaxyproject/galaxy/issues/9265 | 24 January 2020, 14:24:51 UTC |
| d672951 | Nicola Soranzo | 23 January 2020, 21:57:54 UTC | Simplify and refactor | 23 January 2020, 21:57:54 UTC |
| e227b14 | mvdbeek | 23 January 2020, 15:02:52 UTC | Fix unselected select parameter comparison to empty string `$wrapper == ""` and `$wrapper == "None"` had been valid ways to check for unselected / optional select parameters. This restores the `$wrapper == ""` form as used by gffcompare https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41 | 23 January 2020, 19:24:52 UTC |
| 1a6d98d | Björn Grüning | 23 January 2020, 18:12:28 UTC | Merge pull request #9260 from mvdbeek/fix_multi_select_equals_empty_string [20.01] Fix unselected select parameter comparison to empty string | 23 January 2020, 18:12:28 UTC |
| 673f21f | mvdbeek | 23 January 2020, 16:00:38 UTC | Merge branch 'release_19.09' into release_20.01 | 23 January 2020, 16:00:38 UTC |
| fc0e318 | Marius van den Beek | 23 January 2020, 15:58:44 UTC | Merge pull request #9253 from bernt-matthias/topic/fix-popen-py3-followup [19.09] fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246 | 23 January 2020, 15:58:44 UTC |
| 5d379dc | mvdbeek | 23 January 2020, 15:02:52 UTC | Fix unselected select parameter comparison to empty string `$wrapper == ""` and `$wrapper == "None"` had been valid ways to check for unselected / optional select parameters. This restores the `$wrapper == ""` form as used by gffcompare https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41 | 23 January 2020, 15:02:56 UTC |
| b7e1c1b | mvdbeek | 22 January 2020, 20:43:39 UTC | Also mkdir -p configs | 22 January 2020, 20:43:39 UTC |
| 60d8c46 | mvdbeek | 22 January 2020, 17:48:01 UTC | Make tools that manipulate files in configs/ resubmittable | 22 January 2020, 18:02:23 UTC |
| 96aabc1 | mvdbeek | 22 January 2020, 17:46:05 UTC | Make mounting configs dir conditional on tool profile | 22 January 2020, 18:02:23 UTC |
| 7bbdf83 | mvdbeek | 18 January 2020, 11:49:23 UTC | Mount job_working_directory/configs rw Many tools have this pattern where they move the config file somewhere, which doesn't work if it is mounted read-only. | 22 January 2020, 16:40:22 UTC |
| c358e3a | M Bernt | 22 January 2020, 15:54:48 UTC | remove space Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com> | 22 January 2020, 15:54:48 UTC |
| db5bd4f | M Bernt | 22 January 2020, 15:16:45 UTC | fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246 | 22 January 2020, 15:16:45 UTC |
| 54d6bad | mvdbeek | 22 January 2020, 15:08:45 UTC | Merge branch 'release_19.09' into release_20.01 | 22 January 2020, 15:08:45 UTC |
| a52e24e | John Chilton | 22 January 2020, 14:02:45 UTC | Merge pull request #9245 from mvdbeek/fix_deletion_of_outputs_before_job [20.01] Fix deletion of outputs and working before job | 22 January 2020, 14:02:45 UTC |
| d6a077c | John Chilton | 22 January 2020, 14:02:02 UTC | Merge pull request #9243 from mvdbeek/fix_data_table_moving [19.09] Fix moving of data manager output for entries | 22 January 2020, 14:02:02 UTC |
| dc7e2e5 | Marius van den Beek | 22 January 2020, 12:28:53 UTC | Merge pull request #9246 from bernt-matthias/topic/fix-popen-py3 [19.09] python3 fixes for setups using drmaa and realuser setups | 22 January 2020, 12:28:53 UTC |
| 2adf6a8 | Nicola Soranzo | 22 January 2020, 12:24:39 UTC | Merge branch 'release_19.09' into release_20.01 | 22 January 2020, 12:24:39 UTC |
| 8e81af2 | mvdbeek | 22 January 2020, 10:49:06 UTC | Update xsd for filename attribute on configfiles | 22 January 2020, 10:49:06 UTC |
| 95144e5 | M Bernt | 22 January 2020, 10:29:10 UTC | Add parentheses for import Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com> | 22 January 2020, 10:29:10 UTC |
| 9e76dcd | mvdbeek | 22 January 2020, 10:16:06 UTC | Things are nicer on python 3 | 22 January 2020, 10:16:06 UTC |
| 3568629 | mvdbeek | 22 January 2020, 09:59:14 UTC | Ignore FileNotFoundError when deleting extra files This worked previously but logged an exception, causing further cleanup to be skipped. | 22 January 2020, 09:59:17 UTC |
| 3d868e0 | mvdbeek | 22 January 2020, 09:52:38 UTC | Use context manager for writing param_file | 22 January 2020, 09:54:49 UTC |
| 5bb2d16 | M Bernt | 22 January 2020, 09:37:20 UTC | fix import order | 22 January 2020, 09:37:20 UTC |
| 83a8e1b | mvdbeek | 22 January 2020, 09:20:27 UTC | Test that working dir is intact on resubmission | 22 January 2020, 09:25:16 UTC |
| 9a5004c | mvdbeek | 22 January 2020, 08:43:11 UTC | Place configfiles in working dir if filename set | 22 January 2020, 08:43:15 UTC |
| 5de147a | M Bernt | 18 January 2020, 16:57:50 UTC | re-remove the data input | 22 January 2020, 08:37:24 UTC |
| fff8d2e | M Bernt | 18 January 2020, 13:43:38 UTC | inputs configfile: test for filename and data_style attributes | 22 January 2020, 08:37:19 UTC |
| 71788d0 | mvdbeek | 22 January 2020, 08:35:57 UTC | Simplify PREPARE_DIRS logic | 22 January 2020, 08:35:57 UTC |
| 4c8918a | John Chilton | 21 January 2020, 20:16:34 UTC | Merge pull request #9232 from dannon/mailto_hrefs_in_menus [20.01] Fix mailto hrefs in menus | 21 January 2020, 20:16:34 UTC |
| be3e07f | M Bernt | 21 January 2020, 18:12:59 UTC | fix Popen/py3 related bugs for real user setups - Popen returns bytes in python3 - strings are needed analoguous to what is happening in slurm I use unicodify here | 21 January 2020, 18:12:59 UTC |
| 28277d2 | mvdbeek | 21 January 2020, 10:57:20 UTC | Fix unit test | 21 January 2020, 10:57:20 UTC |
| 9e4545f | mvdbeek | 21 January 2020, 10:04:37 UTC | Copy working/ and outputs/ before starting job script This seems to be the most robust way to make sure that resubmission by the DRM will start with proper configfiles and pre-populated outputs (OutputParameterJSONTool). The cost should be minimal as most of the time these are empty directories. This would also help with https://github.com/galaxyproject/galaxy/pull/9236#issuecomment-576050103 | 21 January 2020, 10:18:23 UTC |
| 8d099ef | mvdbeek | 21 January 2020, 09:47:50 UTC | Only delete writable files on job resubmission | 21 January 2020, 10:18:13 UTC |
| db472b2 | mvdbeek | 20 January 2020, 18:29:31 UTC | Only delete working/ and outputs on resubmission | 21 January 2020, 10:16:38 UTC |
| f327189 | mvdbeek | 20 January 2020, 16:30:35 UTC | Fix moving of data manager output for entries https://github.com/galaxyproject/galaxy/pull/8250 introduced the add and remove keys for removing items from a data table. If there is a single data table definition incoming (meaning a dictionary) that does not specify the `add` key the new code would just ignore that entry and not move it. Fixes https://github.com/galaxyproject/tools-iuc/issues/2783? | 20 January 2020, 16:36:12 UTC |
| 47c5a0e | Nicola Soranzo | 19 January 2020, 23:01:53 UTC | Merge pull request #9239 from mvdbeek/fix_binary_upload_problems_with_faulty_headers [19.09] Fallback to binary download if header lies about content encoding | 19 January 2020, 23:01:53 UTC |
| 4d686ed | Marius van den Beek | 19 January 2020, 18:59:20 UTC | Simplify use_source_encoding logic Thanks Nicola, very nice! Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 19 January 2020, 18:59:20 UTC |
| 933c3ba | Nicola Soranzo | 19 January 2020, 18:12:58 UTC | Merge pull request #9240 from mvdbeek/fix_planemo_lint_error [20.01] Fix lint warning string formatting | 19 January 2020, 18:12:58 UTC |
| 29d73ff | Björn Grüning | 19 January 2020, 16:59:38 UTC | Merge pull request #9237 from mvdbeek/remove_fimo_from_galaxy_lib_unversioned_tools [20.01] Move meme_fimo out of unversioned lib tools | 19 January 2020, 16:59:38 UTC |
| 6e8f143 | mvdbeek | 19 January 2020, 16:47:18 UTC | Fix lint warning string formatting Introduced in https://github.com/mvdbeek/galaxy/commit/c4fabf05e11c033006834fd0bf0d9077c0156134, causes: ``` ValueError: unsupported format character 'n' (0x6e) at index 16 ``` | 19 January 2020, 16:47:23 UTC |
| e6fe571 | mvdbeek | 19 January 2020, 15:40:53 UTC | Fallback to binary download if header lies about content encoding Fixes https://github.com/galaxyproject/galaxy/issues/9238 | 19 January 2020, 15:42:10 UTC |
| 69ff055 | mvdbeek | 19 January 2020, 11:45:15 UTC | Move meme_fimo out of unversioned lib tools | 19 January 2020, 11:46:24 UTC |
| 6a4a3b8 | Dannon Baker | 17 January 2020, 17:57:53 UTC | Formatting. | 17 January 2020, 17:57:53 UTC |
| 6218b31 | Dannon Baker | 16 January 2020, 14:39:45 UTC | Allow mailto addresses (for support/contact) in menu items. | 17 January 2020, 17:57:20 UTC |
| 531ad72 | John Chilton | 17 January 2020, 17:19:48 UTC | Starting work on tool-util 20.1.0.dev4 | 17 January 2020, 17:19:48 UTC |
| 46d772b | John Chilton | 17 January 2020, 17:18:45 UTC | Merge pull request #9228 from mvdbeek/extended_base_aonnotation_fixes [20.01] More mulled-build-files fixes | 17 January 2020, 17:18:45 UTC |
| bc9a840 | mvdbeek | 17 January 2020, 11:22:13 UTC | Turn off determin_base_image for mulled-build-files | 17 January 2020, 11:22:13 UTC |
| d79e746 | mvdbeek | 17 January 2020, 10:20:08 UTC | Delete /usr/local before moving conda env /usr/local/man already exists and is a symlink in bioconda/extended-base-image:latest, and so `cp -R /tmp/conda/*` fails with ``` cp: cannot overwrite non-directory '/usr/local/man' with directory '/tmp/conda/man' ``` | 17 January 2020, 10:20:10 UTC |
| 798219b | Marius van den Beek | 17 January 2020, 09:21:15 UTC | Merge pull request #9225 from nuwang/affinity_and_tolerations [20.01] Fix: Added support for specifying k8s job affinity and tolerations | 17 January 2020, 09:21:15 UTC |
| cc36560 | mvdbeek | 17 January 2020, 08:45:14 UTC | Only cache pip dir, seems integration tests broke because something changed in system python | 17 January 2020, 08:45:14 UTC |
| 5ee23fd | mvdbeek | 17 January 2020, 08:35:16 UTC | Fix mulled-build-files if name_override is not given | 17 January 2020, 08:35:16 UTC |
| 44efbb5 | mvdbeek | 17 January 2020, 08:19:49 UTC | Move base_image_for_targets to when we actually need it This avoids the check for builds that already exist | 17 January 2020, 08:19:52 UTC |
| d99a92d | Nuwan Goonasekera | 16 January 2020, 11:38:51 UTC | Added support for specifying k8s job affinity and tolerations | 16 January 2020, 18:13:40 UTC |
| c0e37c9 | John Chilton | 16 January 2020, 14:54:28 UTC | Starting work on tool-util 20.1.0.dev3 | 16 January 2020, 14:54:28 UTC |
| f8117b0 | John Chilton | 16 January 2020, 14:50:55 UTC | Merge pull request #9224 from mvdbeek/extended_base_aonnotation_fixes [20.01] Extended base annotation fixes | 16 January 2020, 14:50:55 UTC |
| b1885b0 | mvdbeek | 16 January 2020, 10:52:00 UTC | Sort best package by upload time (lowest priority) in addition to version and build number. This is necessary for getting the extended-base annotation for qiime 1.9.1, which does not contain the annotation in linux-64/qiime-1.9.1-np110py27_1.tar.bz2 while in the newer linux-64/qiime-1.9.1-np112py27_1.tar.bz2 it is present. This depends of course on `conda search` returning packages sorted by upload time and is a little brittle. It does seem better than always picking the oldest upload time as we do without this change. Also looks in meta.yaml for extended base annotation, since sometimes this isn't present in info/about.json. | 16 January 2020, 10:52:03 UTC |
| 4db5f18 | John Chilton | 15 January 2020, 18:19:14 UTC | Starting work on tool-util 20.1.0.dev2 | 15 January 2020, 18:19:14 UTC |
| beaa844 | John Chilton | 15 January 2020, 14:55:00 UTC | Merge pull request #9215 from mvdbeek/fix_extended_base_for_singularity_2 [20.01] Fix extended base for singularity and add base_image_for_targets | 15 January 2020, 14:55:00 UTC |
| 0b5095f | Marius van den Beek | 14 January 2020, 20:28:49 UTC | Merge pull request #9219 from nuwang/release_20.01 Fix: Added support for specifying k8s job pod priority class | 14 January 2020, 20:28:49 UTC |
| 254ce7c | Dannon Baker | 14 January 2020, 20:14:26 UTC | Merge remote-tracking branch 'upstream/release_19.09' into release_20.01 | 14 January 2020, 20:14:26 UTC |
| 56362e3 | Dannon | 14 January 2020, 20:13:21 UTC | Merge pull request #9217 from kaukrise/bug_fix_trackster_navbar_overflow Ensure visible overflow on navbar container | 14 January 2020, 20:13:21 UTC |
| 4cbe0ce | Dannon | 14 January 2020, 19:58:20 UTC | Merge pull request #9216 from kaukrise/bug_fix_trackster_history Wrap SQL statement in a text() function as required by sqlalchemy | 14 January 2020, 19:58:20 UTC |
| 0165fb4 | Nuwan Goonasekera | 14 January 2020, 14:54:38 UTC | Added support for specifying k8s job pod priority class | 14 January 2020, 15:06:49 UTC |
| 01befe1 | kaukrise | 14 January 2020, 14:59:42 UTC | Optimise import formatting Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 14 January 2020, 14:59:42 UTC |
| 6f68f2a | Kai Kruse | 14 January 2020, 14:48:14 UTC | Ensure visible overflow on nav ba container so that we can push the genome navigation into the title element. Fixes #9205 | 14 January 2020, 14:48:14 UTC |
| 9bf1bf5 | Kai Kruse | 14 January 2020, 14:46:57 UTC | Wrap SQL statement in a text() function as required by sqlalchemy. Fixes a history loading issue in Trackster #9205 | 14 January 2020, 14:46:57 UTC |
| 6d3b14f | mvdbeek | 14 January 2020, 09:57:20 UTC | Change any_target_requires_extended_base to base_image_for_targets This is easier to use in planemo (we don't need to figure out which image to use based on the return value of any_target_requires_extended_base) and leaves open the possibility for custom base image annotation in conda recipes or other places. | 14 January 2020, 10:01:31 UTC |
| aab4ac2 | mvdbeek | 14 January 2020, 09:48:56 UTC | Pass base image to Singularity template | 14 January 2020, 10:01:20 UTC |
| 49ec518 | John Chilton | 14 January 2020, 04:05:59 UTC | Starting work on tool-util 20.1.0.dev1 | 14 January 2020, 04:05:59 UTC |
| 7890be5 | John Chilton | 14 January 2020, 04:03:48 UTC | Starting work on util 20.1.0.dev1 | 14 January 2020, 04:03:48 UTC |
| 13fbcbe | John Chilton | 14 January 2020, 03:55:16 UTC | Update tool-util requirements (now depends a new galaxy-util). | 14 January 2020, 03:55:16 UTC |
| 0bebd6c | John Chilton | 14 January 2020, 03:48:14 UTC | Prep next release galaxy-util, galaxy-tool-util (20.1.0-dev0). | 14 January 2020, 03:53:18 UTC |
| 9fb80f0 | Nicola Soranzo | 14 January 2020, 03:03:48 UTC | Merge pull request #9210 from mvdbeek/backport_9175 [20.01] Backport 9175: Update galaxy.tool_util.cwl for latest changes in CWL branch. | 14 January 2020, 03:03:48 UTC |
| 8e6c263 | Nicola Soranzo | 14 January 2020, 01:34:00 UTC | Remove code presently unused | 14 January 2020, 01:34:00 UTC |
| bccb068 | Nicola Soranzo | 14 January 2020, 00:27:11 UTC | Flush YAML temp file before loading it | 14 January 2020, 00:27:11 UTC |
| 0af05d7 | Nicola Soranzo | 13 January 2020, 23:54:16 UTC | Fix imports | 13 January 2020, 23:54:16 UTC |
| dd798e8 | Nicola Soranzo | 13 January 2020, 21:39:09 UTC | Merge pull request #9212 from mvdbeek/fix_runtime_error [20.01] Fix runtime error in ToolConfWatcher | 13 January 2020, 21:39:09 UTC |
| 312b896 | John Chilton | 13 January 2020, 20:49:38 UTC | Update lib/galaxy/tool_util/cwl/parser.py Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 13 January 2020, 20:49:38 UTC |
| 478bacf | John Chilton | 13 January 2020, 20:49:16 UTC | Update lib/galaxy/tool_util/cwl/schema.py Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 13 January 2020, 20:49:16 UTC |
| 360cf0c | Nicola Soranzo | 13 January 2020, 19:18:34 UTC | Start with empty hash Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com> | 13 January 2020, 19:18:34 UTC |
| d9f4118 | mvdbeek | 13 January 2020, 17:38:23 UTC | Fix dictionary changed size during iteration error Should prevent ``` Traceback (most recent call last): File "PY3.7/threading.py", line 917, in _bootstrap_inner self.run() File "PY3.7/threading.py", line 865, in run self._target(*self._args, **self._kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 101, in check hashes = {key: None for key in self.paths.keys()} File "lib/galaxy/tools/toolbox/watcher.py", line 101, in <dictcomp> hashes = {key: None for key in self.paths.keys()} RuntimeError: dictionary changed size during iteration ``` We do something similar already in https://github.com/mvdbeek/galaxy/blob/6af20e1b0cac5a3abdcab3be901b4d0a761b9067/lib/galaxy/tools/toolbox/watcher.py#L105 | 13 January 2020, 17:38:26 UTC |
| d69adcf | Nicola Soranzo | 11 January 2020, 21:32:20 UTC | Merge duplicate keys before validating YAML config files xref. https://github.com/galaxyproject/galaxy/issues/8558 For other YAML files, `ordered_load()` will raise an exception when it finds a mapping with duplicate keys. | 13 January 2020, 15:47:31 UTC |
| 5b1769b | Nicola Soranzo | 10 January 2020, 17:53:20 UTC | Always use `yaml.safe_load()` | 13 January 2020, 15:47:31 UTC |
| 8392554 | Nicola Soranzo | 10 January 2020, 11:08:48 UTC | Disable Python 2.7 mulled tests | 13 January 2020, 15:47:31 UTC |
| 3734766 | Nicola Soranzo | 08 January 2020, 00:42:31 UTC | Update cwltool dependencies | 13 January 2020, 15:47:31 UTC |
| a639c93 | Nicola Soranzo | 07 January 2020, 13:33:59 UTC | Filter Python 2 deprecation warning from cwltool which makes some tools fail by printing to stderr: ``` galaxy.tool_util.output_checker DEBUG 2020-01-07 02:59:07,720 job failed, detected state generic_error, standard error is - [/galaxy_venv/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as the Python 2.7 version of cwltool won't be maintained after that date. """, category=CWLToolDeprecationWarning) ] ``` | 13 January 2020, 15:35:40 UTC |
| ebe0b97 | John Chilton | 03 January 2020, 15:40:07 UTC | More fixes for galaxy-tool-util from Planemo test suite. | 13 January 2020, 15:35:36 UTC |
| 5d61fe5 | John Chilton | 02 January 2020, 15:56:59 UTC | Fix schema salad requirement. | 13 January 2020, 15:35:32 UTC |
| 30bf991 | John Chilton | 02 January 2020, 00:17:26 UTC | Fix up bad import of galaxy.model stuff from tool_util. | 13 January 2020, 15:35:27 UTC |
| 8bf557c | John Chilton | 01 January 2020, 17:12:19 UTC | Update galaxy.tool_util.cwl for latest changes in CWL branch. | 13 January 2020, 15:35:23 UTC |
| bb73e3e | John Chilton | 13 January 2020, 15:30:17 UTC | Merge pull request #9202 from mvdbeek/allow_passing_conda_context [20.01] Allow passing conda_context to any_target_requires_extended_base | 13 January 2020, 15:30:17 UTC |
| f32f24e | mvdbeek | 11 January 2020, 20:00:08 UTC | Allow passing in conda_context This makes sense for planemo container_register. | 11 January 2020, 20:00:10 UTC |
| 6e68e16 | John Chilton | 11 January 2020, 16:17:35 UTC | Merge pull request #9199 from mvdbeek/update_mulled_build_files_for_annotating_base_image [20.01] Add base_image column to mulled-build-files | 11 January 2020, 16:17:35 UTC |
