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 |
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 |
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 |
dad5563 | Nicola Soranzo | 06 September 2017, 17:06:07 UTC | Merge branch 'release_16.01' into release_16.04 | 06 September 2017, 17:06:07 UTC |
2207e7f | Dannon Baker | 06 September 2017, 16:35:30 UTC | Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. | 06 September 2017, 16:35:30 UTC |
02c7792 | John Chilton | 06 September 2017, 13:34:11 UTC | [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 | 06 September 2017, 13:34:11 UTC |
2528a89 | Nicola Soranzo | 20 March 2017, 16:54:24 UTC | Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids | 20 March 2017, 16:54:24 UTC |
12eb383 | Martin Cech | 20 March 2017, 14:00:41 UTC | fix xss thanks to @erasche | 20 March 2017, 14:00:41 UTC |
4cf70ae | Nate Coraor | 15 December 2016, 18:04:29 UTC | Merge branch 'release_16.01' into release_16.04 | 15 December 2016, 18:04:29 UTC |
4c07734 | Nate Coraor | 15 December 2016, 17:55:39 UTC | Merge branch 'release_15.10' into release_16.01 | 15 December 2016, 17:55:39 UTC |
95daf69 | Nate Coraor | 15 December 2016, 17:49:39 UTC | Merge branch 'release_15.07' into release_15.10 | 15 December 2016, 17:49:39 UTC |
790e60a | Nate Coraor | 15 December 2016, 17:46:17 UTC | Merge branch 'release_15.05' into release_15.07 | 15 December 2016, 17:46:17 UTC |
7c443ed | Nate Coraor | 15 December 2016, 17:38:28 UTC | Merge branch 'release_15.03' into release_15.05 | 15 December 2016, 17:38:28 UTC |
da7afb4 | Nate Coraor | 15 December 2016, 17:37:10 UTC | Merge branch 'release_15.01' into release_15.03 | 15 December 2016, 17:37:10 UTC |
9ee3d01 | Nate Coraor | 15 December 2016, 17:36:21 UTC | Merge branch 'release_14.10' into release_15.01 | 15 December 2016, 17:36:21 UTC |
c1e3087 | Nate Coraor | 15 December 2016, 17:34:18 UTC | Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. | 15 December 2016, 17:34:18 UTC |
788dc1e | Nicola Soranzo | 07 November 2016, 11:08:54 UTC | Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py | 07 November 2016, 11:14:33 UTC |
a274e63 | Björn Grüning | 05 November 2016, 10:52:03 UTC | Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml | 05 November 2016, 10:52:03 UTC |
c524521 | mvdbeek | 04 November 2016, 19:21:05 UTC | Make catching XML parsing errors python2.6 compatible | 04 November 2016, 19:21:05 UTC |
f6ca913 | mvdbeek | 04 November 2016, 11:49:30 UTC | Log invalid xml filename | 04 November 2016, 16:53:12 UTC |
c94b220 | mvdbeek | 03 November 2016, 16:06:00 UTC | Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. | 04 November 2016, 16:42:16 UTC |
65338b3 | Martin Cech | 03 November 2016, 16:39:04 UTC | Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh | 03 November 2016, 16:39:04 UTC |
6082f79 | Nicola Soranzo | 01 November 2016, 14:19:13 UTC | Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d19e35a6460c65#commitcomment-19642191 | 01 November 2016, 14:19:18 UTC |
2adb98e | Martin Cech | 11 October 2016, 15:37:47 UTC | Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… | 11 October 2016, 15:37:47 UTC |
39fb030 | Marius van den Beek | 11 October 2016, 15:07:23 UTC | Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now | 11 October 2016, 15:07:23 UTC |
224c212 | Nicola Soranzo | 05 October 2016, 17:17:03 UTC | Merge branch 'release_16.01' into release_16.04 | 05 October 2016, 17:17:03 UTC |
f7c3e25 | Björn Grüning | 05 October 2016, 17:15:14 UTC | Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 | 05 October 2016, 17:15:14 UTC |
6d27a3c | Marius van den Beek | 29 August 2016, 08:44:57 UTC | Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh#L61) and perhaps why that bug made it into the release in the first place). | 05 October 2016, 16:16:24 UTC |
45e6949 | John Chilton | 23 September 2016, 13:30:20 UTC | Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix | 23 September 2016, 13:30:20 UTC |
5e7ee28 | Martin Cech | 22 September 2016, 21:48:20 UTC | bump freebayes in test (since it was updated) | 22 September 2016, 21:48:20 UTC |
c06f8c2 | Martin Cech | 22 September 2016, 20:00:51 UTC | correct the method call | 22 September 2016, 20:00:51 UTC |
a78b8bc | Martin Cech | 22 September 2016, 18:55:03 UTC | Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 | 22 September 2016, 18:55:03 UTC |
9b3c061 | Dave B | 22 September 2016, 17:59:11 UTC | [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py | 22 September 2016, 18:54:37 UTC |
b748250 | John Chilton | 20 September 2016, 14:44:37 UTC | Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion | 20 September 2016, 14:44:37 UTC |
1f53c32 | Nicola Soranzo | 19 September 2016, 19:51:22 UTC | Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_dbnsfp_datatypes/tabular_to_dbnsfp.py | 19 September 2016, 19:51:33 UTC |
b50d07d | carlfeberhard | 14 September 2016, 17:23:41 UTC | Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 | 14 September 2016, 17:23:41 UTC |
8bf7256 | Martin Cech | 14 September 2016, 17:20:00 UTC | Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions | 14 September 2016, 17:20:00 UTC |
b301fd4 | carlfeberhard | 14 September 2016, 17:18:46 UTC | Dataset perms: correct comment | 14 September 2016, 17:18:46 UTC |
e7cb0ac | carlfeberhard | 13 September 2016, 17:10:24 UTC | Datasets: test for anon deserialization | 13 September 2016, 17:10:42 UTC |
9636ea1 | carlfeberhard | 13 September 2016, 17:09:11 UTC | Datasets: test for anon access/manage | 13 September 2016, 17:09:11 UTC |
fc3dcf3 | carlfeberhard | 13 September 2016, 17:00:58 UTC | Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks | 13 September 2016, 17:00:58 UTC |
b880359 | carlfeberhard | 12 September 2016, 15:04:39 UTC | Datasets: confirm admin ability to set permissions The power was inside you all along. | 12 September 2016, 15:04:39 UTC |
91a190c | carlfeberhard | 12 September 2016, 14:50:57 UTC | Datasets: allow admin to serialize permissions And updates tests. | 12 September 2016, 14:50:57 UTC |
3492e96 | Martin Cech | 18 August 2016, 14:08:48 UTC | Merge pull request #2811 from nsoranzo/release_16.04_backports [16.04] Two backports | 18 August 2016, 14:08:48 UTC |
a134587 | Dave Bouvier | 08 April 2016, 18:42:20 UTC | Correctly check set_environment declarations when updating repository. | 18 August 2016, 13:08:40 UTC |
1f69bf3 | Nicola Soranzo | 18 August 2016, 13:03:59 UTC | Fix run.sh --daemon Broken in commit d5c52cadfd0007338d4c89f505ff272e9acae9f9 . Partial backport from #2765 . Close #2724. | 18 August 2016, 13:07:26 UTC |
d1c58f7 | Marius van den Beek | 17 August 2016, 07:12:17 UTC | Merge pull request #2800 from jmchilton/dbkey_output_without_cond [16.04] Fix dbkey problem discovered by @hrhotz | 17 August 2016, 07:12:17 UTC |
752df7f | Björn Grüning | 16 August 2016, 18:41:49 UTC | Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… | 16 August 2016, 18:41:49 UTC |
e06cf9a | John Chilton | 16 August 2016, 18:12:17 UTC | Add None check to fill_template... ... as requested by @nsoranzo. | 16 August 2016, 18:12:17 UTC |
0110d5a | John Chilton | 16 August 2016, 18:08:38 UTC | Add a test case to dbkey_output_action.xml. Per @nsoranzo's template and suggestion. | 16 August 2016, 18:08:38 UTC |
88d02db | John Chilton | 16 August 2016, 16:55:56 UTC | Don't fill in a cheetah default if unavailable. ... in metadata hack from #961. | 16 August 2016, 16:55:56 UTC |
510290f | John Chilton | 16 August 2016, 14:34:57 UTC | Add example of regressed 16.04 behavior related to dbkey output actions. | 16 August 2016, 14:34:57 UTC |
43320aa | Dannon Baker | 15 August 2016, 13:41:01 UTC | Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. | 15 August 2016, 16:25:17 UTC |
ceeef39 | Dannon Baker | 12 August 2016, 17:33:36 UTC | Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 | 12 August 2016, 17:33:36 UTC |
d24ce8b | guerler | 04 August 2016, 19:45:06 UTC | Add implicit conversions target extension to hda name when listed as selection option | 12 August 2016, 17:01:45 UTC |
f2f62f3 | Nicola Soranzo | 10 August 2016, 15:19:19 UTC | Merge branch 'release_16.01' into release_16.04 Conflicts: .ci/flake8_blacklist.txt tox.ini | 10 August 2016, 15:19:19 UTC |
68f718d | Martin Cech | 10 August 2016, 15:05:05 UTC | Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package [16.01] Fix misplaced parenthesis | 10 August 2016, 15:05:05 UTC |
f4cb63d | Nicola Soranzo | 10 August 2016, 14:17:17 UTC | Pin flake8 version Do not pin when forward-merging to dev branch. Also ignore .tox/ and eggs/ as in #2650 . | 10 August 2016, 14:17:21 UTC |
33c4025 | Nicola Soranzo | 10 August 2016, 13:34:05 UTC | Fix misplaced parenthesis Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304 | 10 August 2016, 13:34:08 UTC |
a7664f0 | Martin Cech | 08 August 2016, 14:40:38 UTC | Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. | 08 August 2016, 14:40:38 UTC |
b39f214 | John Chilton | 05 August 2016, 17:43:04 UTC | Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. | 05 August 2016, 18:19:22 UTC |
e4ca3bf | Enis Afgan | 28 July 2016, 12:38:37 UTC | Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample | 28 July 2016, 12:38:37 UTC |
5d8d932 | Daniel Blankenberg | 27 July 2016, 16:16:21 UTC | Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) | 27 July 2016, 19:07:27 UTC |
8f978b8 | Martin Cech | 26 July 2016, 21:34:02 UTC | Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes | 26 July 2016, 21:34:02 UTC |
f0024d6 | Dannon Baker | 25 July 2016, 14:15:33 UTC | Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) | 26 July 2016, 20:42:40 UTC |
f8cf81d | Dannon Baker | 25 July 2016, 14:02:43 UTC | Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. | 26 July 2016, 20:42:30 UTC |
28da4b6 | Marius van den Beek | 27 April 2016, 11:44:45 UTC | Fix whitespace and comma use | 26 July 2016, 18:39:46 UTC |
4a83103 | Marius van den Beek | 27 April 2016, 11:20:47 UTC | Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. | 26 July 2016, 18:39:40 UTC |
1de7bec | Dannon Baker | 21 July 2016, 16:29:20 UTC | Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function | 21 July 2016, 16:29:20 UTC |
68a6418 | Martin Cech | 21 July 2016, 16:08:28 UTC | Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix | 21 July 2016, 16:08:28 UTC |
132bd4d | Dannon Baker | 21 July 2016, 12:33:47 UTC | Merge branch 'backport_2613' into release_16.04 (and rebuild client) | 21 July 2016, 12:33:47 UTC |
95c64c0 | Dannon Baker | 19 July 2016, 22:14:15 UTC | Rebuild as a part of merging from 16.01. | 19 July 2016, 22:14:15 UTC |
ac64c01 | Dannon Baker | 19 July 2016, 22:12:47 UTC | Merge branch 'release_16.01' into release_16.04 | 19 July 2016, 22:12:47 UTC |
f4631d2 | Dannon Baker | 19 July 2016, 22:12:17 UTC | Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh | 19 July 2016, 22:12:17 UTC |
85671bd | Eric Enns | 26 June 2016, 17:56:14 UTC | Fixed E302 | 19 July 2016, 18:27:39 UTC |
7e389c7 | Eric Enns | 26 June 2016, 17:45:34 UTC | Fixed E226 | 19 July 2016, 18:27:26 UTC |
09b9339 | Eric Enns | 26 June 2016, 17:42:33 UTC | Fixed to only line_count not line_count + 1 lines and added in really basic test | 19 July 2016, 18:27:09 UTC |
5f24afb | Eric Enns | 26 June 2016, 16:48:09 UTC | Fix off by one error, causing only first line of file to be rendered in peek. | 19 July 2016, 18:26:58 UTC |
0d49b06 | Martin Cech | 19 July 2016, 18:24:16 UTC | repack | 19 July 2016, 18:24:16 UTC |
d550024 | carlfeberhard | 14 July 2016, 13:58:56 UTC | UI, history: more feedback on bad collection type Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js static/scripts/bundled/login.bundled.js.map static/scripts/mvc/history/history-contents.js | 19 July 2016, 18:14:33 UTC |
6547487 | carlfeberhard | 14 July 2016, 13:45:23 UTC | UI, history: implement list:list Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js | 19 July 2016, 18:14:06 UTC |
6b64af7 | carlfeberhard | 09 May 2016, 15:41:56 UTC | UI, history: doc updates Conflicts: client/galaxy/scripts/mvc/history/history-contents.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map | 19 July 2016, 18:13:39 UTC |
e378503 | carlfeberhard | 09 May 2016, 14:17:42 UTC | UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map | 19 July 2016, 18:12:21 UTC |
10ac6ee | Carl Eberhard | 19 July 2016, 17:52:58 UTC | Merge pull request #2556 from ericenns/fix-2461-dataset-peek [16.04] Fix off by one error, causing only first line of file to be rendered … | 19 July 2016, 17:52:58 UTC |
8a5042d | Martin Cech | 19 July 2016, 15:54:54 UTC | Merge pull request #2626 from dannon/backport_hammerthrow [16.04] Backport workflow fix | 19 July 2016, 15:54:54 UTC |
bc79e9c | carlfeberhard | 19 July 2016, 13:51:10 UTC | UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. | 19 July 2016, 13:51:10 UTC |
f941657 | Dannon Baker | 19 July 2016, 13:47:24 UTC | Extra debugging to hopefully shed light on the PJA Async issue with delete intermediates action and new(ish) workflow scheduling. Clarified a few vars. | 19 July 2016, 13:50:02 UTC |
e4a35f9 | Dannon Baker | 19 July 2016, 13:14:57 UTC | Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. | 19 July 2016, 13:14:57 UTC |
dfce1a9 | Dannon Baker | 15 June 2016, 15:57:33 UTC | This is an extra hammer swing at #1531 / #1542, which @rmarenco encountered. He said this resolves it. | 18 July 2016, 22:40:26 UTC |
92948b5 | guerler | 18 July 2016, 18:15:48 UTC | Overload select wrapper`s concat function | 18 July 2016, 18:15:48 UTC |
8c59d1c | Björn Grüning | 15 July 2016, 21:52:49 UTC | Merge pull request #2618 from nsoranzo/release_16.04_fix_download_binary [16.04] Strip whitespaces when processing <url_template> content | 15 July 2016, 21:52:49 UTC |
aa7ead6 | Nicola Soranzo | 14 July 2016, 18:18:43 UTC | Strip whitespaces when processing <url_template> content Otherwise download_binary action tries to save the file to an invalid filename. Reported by @remimarenco on IRC. Fix typo. | 14 July 2016, 18:43:40 UTC |
05c063b | Martin Cech | 08 July 2016, 18:49:57 UTC | Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes | 08 July 2016, 18:49:57 UTC |