| e0a06a3 | Nicola Soranzo | 12 December 2019, 17:48:38 UTC | Merge branch 'release_17.01' into release_17.05 | 12 December 2019, 17:48:38 UTC |
| 61e6fd1 | Nicola Soranzo | 12 December 2019, 17:43:26 UTC | Merge branch 'release_16.10' into release_17.01 | 12 December 2019, 17:43:26 UTC |
| 267037f | Nicola Soranzo | 12 December 2019, 17:42:02 UTC | Merge branch 'release_16.07' into release_16.10 | 12 December 2019, 17:42:02 UTC |
| 6c02000 | Nicola Soranzo | 12 December 2019, 17:30:59 UTC | Merge branch 'release_16.04' into release_16.07 | 12 December 2019, 17:30:59 UTC |
| 48510a2 | John Chilton | 12 December 2019, 16:37:38 UTC | Merge pull request #9089 from nsoranzo/release_16.04_extra-index-url [16.04] Explicitly include PyPI as an ``--extra-index-url`` to pip | 12 December 2019, 16:37:38 UTC |
| aca9490 | Nicola Soranzo | 10 December 2019, 23:21:29 UTC | Explicitly include PyPI as an ``--extra-index-url`` to pip Backport combining commits 244fc834cd4dd3980cc3edb755d22ca5a9372421 and 09fdac513d59ca6dad440616a53daa97751ff905 . This is now needed because wheels.galaxyproject.org is not a full-fledged pypiserver any more but just an S3 bucket served via a CDN. | 10 December 2019, 23:29:06 UTC |
| 06cfb7e | Nicola Soranzo | 16 December 2018, 22:43:37 UTC | Merge branch 'release_17.01' into release_17.05 | 16 December 2018, 22:43:37 UTC |
| 1b30a9a | Nicola Soranzo | 16 December 2018, 22:42:04 UTC | Merge branch 'release_16.10' into release_17.01 | 16 December 2018, 22:42:04 UTC |
| a2e70ef | Nicola Soranzo | 16 December 2018, 22:40:26 UTC | Merge branch 'release_16.07' into release_16.10 | 16 December 2018, 22:40:26 UTC |
| f3c8181 | Nicola Soranzo | 16 December 2018, 22:36:18 UTC | Merge branch 'release_16.04' into release_16.07 | 16 December 2018, 22:36:18 UTC |
| 87fa609 | Nicola Soranzo | 16 December 2018, 22:29:19 UTC | Merge branch 'release_16.01' into release_16.04 | 16 December 2018, 22:29:19 UTC |
| 8f14121 | Nicola Soranzo | 16 December 2018, 22:28:21 UTC | Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 | 16 December 2018, 22:28:21 UTC |
| efe8475 | Nicola Soranzo | 26 November 2018, 16:30:00 UTC | Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 | 11 December 2018, 22:22:01 UTC |
| b10cfa4 | Nate Coraor | 20 May 2016, 13:44:55 UTC | Remove unused $GXPIP_VERSION | 11 December 2018, 22:01:24 UTC |
| 0e5c96e | Nate Coraor | 19 May 2016, 18:42:52 UTC | Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). | 11 December 2018, 22:01:13 UTC |
| c4150d2 | Dannon Baker | 28 September 2018, 16:38:23 UTC | Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 | 28 September 2018, 16:38:23 UTC |
| fa7f2a4 | Dannon Baker | 28 September 2018, 16:37:49 UTC | Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 | 28 September 2018, 16:37:49 UTC |
| 809ae58 | Dannon Baker | 28 September 2018, 16:37:20 UTC | Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 | 28 September 2018, 16:37:20 UTC |
| 8a1616a | Dannon Baker | 28 September 2018, 16:36:48 UTC | Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 | 28 September 2018, 16:36:48 UTC |
| 482f1ea | Dannon Baker | 28 September 2018, 16:35:30 UTC | Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 | 28 September 2018, 16:35:30 UTC |
| f3ba9e2 | John Chilton | 28 September 2018, 16:09:38 UTC | Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method | 28 September 2018, 16:09:38 UTC |
| 814c7f9 | Dannon Baker | 28 September 2018, 15:50:18 UTC | Drop unused peek method (this used unencoded ids) | 28 September 2018, 15:50:18 UTC |
| d80e60c | Dannon | 23 April 2018, 19:59:32 UTC | Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc | 23 April 2018, 19:59:32 UTC |
| 36a182a | Nicola Soranzo | 20 April 2018, 23:21:28 UTC | Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . | 21 April 2018, 00:12:22 UTC |
| 3442196 | Björn Grüning | 31 January 2018, 09:15:01 UTC | Merge pull request #5406 from mvdbeek/conda_and_channel_order_update [17.05] Follow IUC and drop r channel from default conda channels | 31 January 2018, 09:15:01 UTC |
| a70f287 | mvdbeek | 29 January 2018, 17:07:29 UTC | Remove r channel from more locations | 29 January 2018, 17:07:29 UTC |
| 414c031 | mvdbeek | 29 January 2018, 16:35:49 UTC | Follow IUC and Drop r channel from default cond channels | 29 January 2018, 16:35:49 UTC |
| 4288e96 | Dannon Baker | 22 January 2018, 18:20:22 UTC | Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form | 22 January 2018, 18:20:22 UTC |
| d1510c7 | Marius van den Beek | 01 January 2018, 10:57:39 UTC | Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs [17.05] Provide UI collection output information for subworkflows. | 01 January 2018, 10:57:39 UTC |
| cb9fe3e | Martin Cech | 20 December 2017, 18:23:28 UTC | implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon | 20 December 2017, 18:23:28 UTC |
| 40a5ddd | Martin Cech | 20 December 2017, 16:37:22 UTC | fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend | 20 December 2017, 16:37:22 UTC |
| bb39b7d | John Chilton | 08 December 2017, 20:34:26 UTC | Provide UI collection output information for subworkflows. This fixes #5158 and should provide more correct extension based connection information as well. Includes a backport of #4346 which fixes #3120. | 08 December 2017, 20:46:33 UTC |
| 86ab6fd | Nicola Soranzo | 07 December 2017, 15:47:13 UTC | Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. | 07 December 2017, 15:47:13 UTC |
| fd223e3 | John Chilton | 06 December 2017, 16:25:28 UTC | Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. | 06 December 2017, 16:25:47 UTC |
| eab30c9 | John Chilton | 15 November 2017, 01:27:25 UTC | Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 | 15 November 2017, 01:27:25 UTC |
| 54b9b09 | John Chilton | 15 November 2017, 01:25:38 UTC | Merge remote-tracking branch 'upstream/release_16.10' into HEAD | 15 November 2017, 01:25:38 UTC |
| 4a28142 | John Chilton | 15 November 2017, 01:23:44 UTC | Merge remote-tracking branch 'upstream/release_16.07' into HEAD | 15 November 2017, 01:23:44 UTC |
| 9a13a4a | John Chilton | 15 November 2017, 01:22:42 UTC | Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override | 15 November 2017, 01:22:42 UTC |
| 63f039b | Martin Cech | 14 November 2017, 19:15:22 UTC | remove the default override since it is wrong and ignores the access permissions | 14 November 2017, 19:15:22 UTC |
| e5587dc | Dannon Baker | 13 November 2017, 16:35:34 UTC | Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags [17.05][BUG] Specify TagAssociation class when copying a tag | 13 November 2017, 16:35:34 UTC |
| 6915007 | Dannon Baker | 13 November 2017, 14:20:02 UTC | Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher | 13 November 2017, 14:20:02 UTC |
| 0207b01 | mvdbeek | 11 November 2017, 19:48:12 UTC | Specify TagAssociation class when copying a tag This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags. | 11 November 2017, 19:53:13 UTC |
| b6a0a1b | mvdbeek | 11 November 2017, 09:15:39 UTC | Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. | 11 November 2017, 09:43:03 UTC |
| 7688b05 | Nicola Soranzo | 30 October 2017, 18:50:14 UTC | Merge branch 'release_17.01' into release_17.05 | 30 October 2017, 18:50:14 UTC |
| c7b09f8 | Nicola Soranzo | 30 October 2017, 18:49:17 UTC | Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt | 30 October 2017, 18:49:17 UTC |
| a537aa4 | Nicola Soranzo | 30 October 2017, 18:41:25 UTC | Merge pull request #4749 from mvdbeek/conda_mapping_path_fix [17.05] Fix path to example conda mapping | 30 October 2017, 18:41:25 UTC |
| 7bf2bbf | John Chilton | 27 October 2017, 15:31:49 UTC | Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. | 27 October 2017, 15:31:49 UTC |
| aef5f4f | John Chilton | 26 October 2017, 16:56:46 UTC | [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. | 26 October 2017, 16:56:59 UTC |
| 20621b7 | Nicola Soranzo | 25 October 2017, 18:07:46 UTC | Merge branch 'release_17.01' into release_17.05 | 25 October 2017, 18:07:46 UTC |
| a7bf160 | Nicola Soranzo | 25 October 2017, 18:05:24 UTC | Merge branch 'release_16.10' into release_17.01 | 25 October 2017, 18:05:24 UTC |
| 90289b6 | Nicola Soranzo | 25 October 2017, 18:03:52 UTC | Merge branch 'release_16.07' into release_16.10 | 25 October 2017, 18:03:52 UTC |
| e3e28dd | Nicola Soranzo | 25 October 2017, 18:02:00 UTC | Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... | 25 October 2017, 18:02:00 UTC |
| 7e08ba6 | John Chilton | 25 October 2017, 16:08:03 UTC | Rework in_directory fix to move realpath expansion into galaxy.util. | 25 October 2017, 16:08:03 UTC |
| 95f8f48 | John Chilton | 25 October 2017, 14:43:54 UTC | Doc fix thanks to @nsoranzo. | 25 October 2017, 14:43:54 UTC |
| fcb23eb | John Chilton | 25 October 2017, 14:34:35 UTC | Some documentation to clarify discussion on #4856. | 25 October 2017, 14:34:35 UTC |
| 4b5dc39 | John Chilton | 25 October 2017, 14:31:07 UTC | Add basic test for in_directory. | 25 October 2017, 14:32:20 UTC |
| 899b0d8 | John Chilton | 25 October 2017, 02:48:02 UTC | Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. | 25 October 2017, 02:49:24 UTC |
| a4a8f15 | John Chilton | 25 October 2017, 01:55:23 UTC | Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API | 25 October 2017, 01:55:23 UTC |
| 9791dd2 | Nicola Soranzo | 24 October 2017, 18:34:40 UTC | Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 | 24 October 2017, 18:36:19 UTC |
| b35fe93 | Nate Coraor | 23 October 2017, 14:31:20 UTC | Merge branch 'release_17.01' into release_17.05 | 23 October 2017, 14:31:20 UTC |
| c4855af | Nate Coraor | 23 October 2017, 14:30:33 UTC | Merge branch 'release_16.10' into release_17.01 | 23 October 2017, 14:30:33 UTC |
| dda175d | Nate Coraor | 23 October 2017, 14:29:59 UTC | Merge branch 'release_16.07' into release_16.10 | 23 October 2017, 14:29:59 UTC |
| cded493 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:27:58 UTC |
| 9f8d3ee | Nate Coraor | 29 September 2017, 18:00:46 UTC | Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability. | 19 October 2017, 14:27:56 UTC |
| e8a7225 | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:27:53 UTC |
| 658f126 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:49 UTC |
| 1bccbef | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:44 UTC |
| 9e672f9 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:28 UTC |
| ed045cd | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:23 UTC |
| 0e69881 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:14 UTC |
| 93a8bfc | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:08 UTC |
| f0e9767 | Nate Coraor | 19 October 2017, 13:14:02 UTC | Merge remote-tracking branch 'origin/release_17.01' into release_17.05 | 19 October 2017, 13:14:02 UTC |
| ae14094 | Nate Coraor | 19 October 2017, 13:13:31 UTC | Merge remote-tracking branch 'origin/release_16.10' into release_17.01 | 19 October 2017, 13:13:31 UTC |
| 34344a7 | Nate Coraor | 19 October 2017, 13:12:07 UTC | Merge remote-tracking branch 'origin/release_16.07' into release_16.10 | 19 October 2017, 13:12:07 UTC |
| 8e199a3 | Marius van den Beek | 19 October 2017, 13:07:33 UTC | Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases | 19 October 2017, 13:07:33 UTC |
| 6d89482 | Nate Coraor | 16 October 2017, 19:09:15 UTC | Additional hardening for older releases | 18 October 2017, 16:54:34 UTC |
| ef203a6 | Nicola Soranzo | 17 October 2017, 16:33:32 UTC | Merge pull request #4816 from natefoo/backport-hardening-17.05 [17.05] Various bits of hardening from #4604 | 17 October 2017, 16:33:32 UTC |
| 9241c9e | Nate Coraor | 17 October 2017, 13:57:48 UTC | Merge remote-tracking branch 'origin/release_17.01' into backport-hardening-17.05 | 17 October 2017, 13:57:48 UTC |
| 66820a4 | E Rasche | 13 September 2017, 06:03:55 UTC | Backport of hardening fixes to 17.05 | 17 October 2017, 13:07:10 UTC |
| 54d3994 | Nicola Soranzo | 17 October 2017, 00:04:53 UTC | Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 | 17 October 2017, 00:04:53 UTC |
| 25fc098 | Nate Coraor | 16 October 2017, 12:59:58 UTC | Merge branch 'release_16.10' into backport-hardening-17.01 | 16 October 2017, 12:59:58 UTC |
| d8ee1a9 | Nate Coraor | 15 October 2017, 02:29:47 UTC | Revert ignoring I201 from 16.10 in 17.01 | 15 October 2017, 02:29:47 UTC |
| 950f926 | Nate Coraor | 14 October 2017, 02:45:45 UTC | Add missing backport of hardening to scripts/grt.py | 15 October 2017, 02:28:09 UTC |
| 9955c4d | Nate Coraor | 13 October 2017, 23:50:42 UTC | Ignore I201 errors in 16.10 | 15 October 2017, 02:27:49 UTC |
| 24c8a26 | Nate Coraor | 13 October 2017, 16:19:25 UTC | Fix backport issues | 15 October 2017, 02:26:09 UTC |
| b13f5d7 | E Rasche | 28 September 2017, 08:07:55 UTC | Rebase script integrity check improvements (#4720) from dev | 15 October 2017, 02:26:07 UTC |
| 7ad6182 | Nate Coraor | 13 October 2017, 16:10:19 UTC | Fix additional uses of subprocess shell=True | 15 October 2017, 02:25:41 UTC |
| f9213b1 | John Chilton | 26 September 2017, 11:57:37 UTC | Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. | 15 October 2017, 02:25:37 UTC |
| 03087e5 | E Rasche | 13 September 2017, 06:03:55 UTC | Rebase hardening commits from dev | 15 October 2017, 02:24:01 UTC |
| 139ba7c | John Chilton | 09 October 2017, 19:28:39 UTC | Pin pydocstyle... | 15 October 2017, 02:23:57 UTC |
| b04aafa | Nicola Soranzo | 14 October 2017, 13:44:38 UTC | Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 | 14 October 2017, 13:44:38 UTC |
| 6d8f8ec | Nate Coraor | 14 October 2017, 02:45:45 UTC | Add missing backport of hardening to scripts/grt.py | 14 October 2017, 02:45:45 UTC |
| 8d573db | Nicola Soranzo | 26 April 2017, 11:46:21 UTC | Use container-based infrastructure (sudo: false) in TravisCI | 13 October 2017, 23:50:55 UTC |
| 3bb5d82 | Nate Coraor | 13 October 2017, 23:50:42 UTC | Ignore I201 errors in 16.10 | 13 October 2017, 23:50:42 UTC |
| 36b974c | John Chilton | 09 October 2017, 19:28:39 UTC | Pin pydocstyle... | 13 October 2017, 19:40:53 UTC |
| fe9839b | Nicola Soranzo | 11 August 2017, 10:53:48 UTC | Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . | 13 October 2017, 19:40:52 UTC |
| d70713d | Nicola Soranzo | 24 January 2017, 17:00:11 UTC | Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. | 13 October 2017, 19:40:52 UTC |
| ef26802 | E Rasche | 13 September 2017, 06:03:55 UTC | Hardening backport differences from dev present in 16.10 but not 16.07 | 13 October 2017, 19:40:52 UTC |
| e60f324 | Nate Coraor | 13 October 2017, 18:56:55 UTC | Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 | 13 October 2017, 18:56:55 UTC |
| f925ffe | Nicola Soranzo | 13 October 2017, 18:09:39 UTC | Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 | 13 October 2017, 18:09:39 UTC |
