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Author SHA1 Message Date
Alexander OSTROVSKY efebceb7c1 ckpt as a subclass 2019-05-15 09:16:55 -04:00
Alexander OSTROVSKY 3cecb466c6 tensorflow checkpoint file support 2019-05-14 16:50:51 -04:00
Martin Cech 3b3b52f013 Merge pull request #7935 from guerler/revise_data_dialog 
Remove view button, fix library flag in data dialog
 2019-05-13 11:05:33 -04:00
Nicola Soranzo 97a3a75339 Merge branch 'release_19.05' into dev 2019-05-13 00:15:00 +01:00
Marius van den Beek 7602bfae7e Merge pull request #7933 from nsoranzo/release_19.05_fix_vcf.gz_upload 
[19.05] Fix upload of gzipped VCF files
 2019-05-12 17:49:18 +02:00
guerler 4a7f6319e9 Adjust dialog test cases 2019-05-11 15:58:38 -04:00
guerler 4180675732 Format code, remove previous label test 2019-05-11 13:21:19 -04:00
Nicola Soranzo c82749688e Merge branch 'release_19.05' into dev 2019-05-11 14:05:55 +01:00
guerler 38856678c1 Remove view icon, focus on selecting datasets only, use folder icon 2019-05-10 21:29:24 -04:00
Marius van den Beek fb53953a87 Merge pull request #7934 from nsoranzo/release_19.05_followup_on_7796 
[19.05] Fix doc building
 2019-05-10 22:43:19 +02:00
Marius van den Beek 99a86eaf10 Merge pull request #7917 from dannon/release_static_fixes 
[19.05] Interactive Environment Fixes
 2019-05-10 21:52:55 +02:00
Nicola Soranzo 391c1296d8 Fix doc building 
Fix the following error when running `make docs`:

```
python parse_gx_xsd.py schema_template.md ../lib/galaxy/tools/xsd/galaxy.xsd > source/dev/schema.md
Traceback (most recent call last):
  File "parse_gx_xsd.py", line 214, in <module>
    main()
  File "parse_gx_xsd.py", line 31, in main
    content_list.append(tag.build_help())
  File "parse_gx_xsd.py", line 84, in build_help
    tag_help.write(_build_tag(tag, self.hide_attributes))
  File "parse_gx_xsd.py", line 99, in _build_tag
    header_level = int(header_level)
ValueError: invalid literal for int() with base 10: 'refresh_on_change'
Makefile:46: recipe for target 'source/dev/schema.md' failed
make[1]: *** [source/dev/schema.md] Error 1
```

Broken in commit 780b07f505 .
 2019-05-10 19:59:45 +01:00
Nicola Soranzo 196e000191 Fix upload of gzipped VCF files 
which were mistakenly sniffed as `vcf_bgzip`.

Fix Fix https://github.com/galaxyproject/galaxy/issues/4892 .
 2019-05-10 19:47:48 +01:00
Dannon Baker 349ac80412 Include suggestion from Marius to make port specification more clear. 2019-05-10 10:12:27 -04:00
Dannon Baker a1487d733a Fix a few more random typos in config, rebuild 2019-05-10 10:09:10 -04:00
Dannon Baker 6bc802307f Document the modern docker networking special DNS 'host.docker.internal' for use with GIES. Fix another typo I saw. 2019-05-10 10:04:12 -04:00
Dannon e8c95a020a Merge pull request #7929 from guerler/welcome_background_white 
Use transparent background in default welcome page
 2019-05-10 08:21:59 -04:00
guerler d2bbd274f0 Increase padding in default welcome center page 2019-05-09 23:33:32 -04:00
guerler e30b824fd6 Use cross-icon instead of clear label in search field 2019-05-09 20:18:48 -04:00
guerler fec2baad26 Fix library flag handling, explicitly set to boolean 2019-05-09 20:11:52 -04:00
guerler ddae8f1c2b Hide Ok button if only one item can be selected 2019-05-09 20:07:09 -04:00
guerler cb4d87f5f8 Transparent default welcome background 2019-05-09 19:44:01 -04:00
Dannon 9c226c783d Merge pull request #43 from mvdbeek/dannon-release_static_fixes 
Fix byte-unicode issue when using Popen
 2019-05-09 15:15:00 -04:00
mvdbeek 502bbb453b Fix byte-unicode issue when using Popen 2019-05-09 21:11:14 +02:00
Dannon Baker c7bc50f6d1 Drop redundant GET (test_ie_avail already does this to check for access) for RStudio custom js 2019-05-09 14:24:19 -04:00
Martin Cech eaacd9e8a1 Merge pull request #7878 from inkuzmin/look-and-feel-in-dataset-libraries 
Look and Feel in Dataset Libraries
 2019-05-09 13:04:53 -04:00
Ivan Kuzmin b50d5c8709 handle case with no libraries 2019-05-09 17:56:00 +03:00
Dannon 1d5bddd8f8 Merge pull request #7908 from guerler/fix_ftp_dialog 
Fix help text in ftp-uploader dialog
 2019-05-09 10:29:40 -04:00
Dannon ccab5f9ac3 Merge pull request #7923 from WilliamHolden/fix_community_tags 
[19.05] Fix community tags showing JSON file
 2019-05-09 09:55:35 -04:00
Dannon 4478ef88eb Merge pull request #7925 from erasche/fix-default-image 
[19.05] Fix default image
 2019-05-09 09:51:17 -04:00
Helena Rasche 9ec128c35d fix image location 2019-05-09 15:34:12 +02:00
Marius van den Beek ceb8c7a637 Merge pull request #7918 from nsoranzo/update_conda_update_docs 
Update instructions on conda upgrade
 2019-05-09 13:59:33 +02:00
Ivan Kuzmin 07b1dadf48 try to use more specific selectors 2019-05-09 13:39:02 +03:00
William Holden 785f2167b9 remove comment 2019-05-08 22:00:19 +00:00
William Holden d3ae6adeaf fix community tags issue 2019-05-08 21:58:16 +00:00
John Chilton b191aec413 Merge pull request #7916 from mvdbeek/fix_gff2bed_things 
[19.05] Remove GFF headers during conversion and test fix
 2019-05-08 15:10:05 -04:00
Martin Cech 3fcc0bed37 Merge branch 'release_19.05' into dev 2019-05-08 14:18:09 -04:00
Martin Cech 5dec2a3c56 Merge pull request #7867 from mvdbeek/fix_scope_issue_for_py3_list_comprehensions 
[19.05] Run futurize for python2 cheetah templates, fix scope issue for py3 comprehensions
 2019-05-08 14:17:54 -04:00
Martin Cech 64b7fd603e Merge pull request #7909 from jmchilton/dev_merge_2 
Merge release_19.05 into dev.
 2019-05-08 14:14:28 -04:00
Nicola Soranzo 8a2abb867f Update instructions on conda upgrade 
Reported by @William-Brown .
 2019-05-08 18:54:55 +01:00
Dannon Baker c90642d969 Cleanup in IE javascript. 2019-05-08 12:43:21 -04:00
Dannon Baker be30834d90 Add bridge for Toast/toastr for use by IE plugins 2019-05-08 12:32:01 -04:00
Dannon Baker a9b1a0454d Update documentation for IES 2019-05-08 11:59:16 -04:00
Martin Cech 375e65ef2b add default to test job_conf 2019-05-08 11:55:13 -04:00
Dannon Baker 9a8cd97379 Delete temporary require.js 2019-05-08 11:49:44 -04:00
Dannon Baker e391f241cd Swap all IES to require-less loading. 2019-05-08 11:49:00 -04:00
mvdbeek 8337f55e21 Fix tests for bed2gff 
and use single-quotes for path, remove deprecated inpterpreter
attribute.
Fixes https://jenkins.galaxyproject.org/job/docker-main-tools-py3/248/
 2019-05-08 17:45:10 +02:00
John Chilton b59fc06d22 Remove GFF headers during conversion. 
Fixes #7771.
 2019-05-08 17:44:52 +02:00
Dannon Baker bc2a84a4dd Swap jupyter to require-free loading. 2019-05-08 11:40:05 -04:00
Dannon Baker fd75ce5e43 Standardize (at least a step forward) access to IES lib via bundle 2019-05-08 10:59:34 -04:00