Dannon Baker
21eac0d445
Merge pull request #4515 from jmchilton/another_merge_issue
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Fix subdirectory listing for extra files
2017-08-30 09:29:18 -04:00
John Chilton
2d9ae75cae
Fix another bad merge issue?
2017-08-29 15:48:19 -04:00
Dannon Baker
d56fcf6777
Merge pull request #4508 from jmchilton/dev_merge_fix
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Fix bad merge of security patch from 17.05 into dev.
2017-08-28 16:55:34 -04:00
John Chilton
2ede34659b
Fix bad merge of security patch from 17.05 into dev.
2017-08-28 16:28:27 -04:00
Dannon Baker
15b1a41df8
Merge pull request #4506 from martenson/merge-release1705
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Merge release_17.05 to dev
2017-08-28 13:18:30 -04:00
Martin Cech
8aefa9d495
repack client
2017-08-28 12:40:43 -04:00
Martin Cech
9337c9fdc1
Merge branch 'release_17.05' into merge-release1705
2017-08-28 12:36:41 -04:00
Martin Cech
f159df391e
Merge pull request #4501 from erasche/2017-08-security
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2017-08 Security Patch
2017-08-28 09:48:51 -04:00
Dannon Baker
4b9b14979a
Merge pull request #4470 from erasche/retheme
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Nicer tool click targets for base + "plain" theme
2017-08-28 09:43:16 -04:00
E Rasche
e6155367e6
2017-08 Security Patch
2017-08-28 10:58:33 +02:00
E Rasche
1d485390b0
2017-08 Security Patch
2017-08-28 10:53:47 +02:00
Dannon Baker
c70926445f
Merge pull request #4483 from guerler/fix_workflow_validation
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[17.05] Validate workflow step after step argument injection
2017-08-25 19:25:08 -04:00
Eric Rasche
426aa310fd
Merge pull request #4486 from dannon/copy_history_minor_improvement
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Minor copy datasets dialog improvement.
2017-08-25 18:45:54 +02:00
E Rasche
97ee0f1fcd
rebuild style
2017-08-25 16:43:12 +00:00
Eric Rasche
0010f6c0d8
Merge pull request #4466 from bgruening/mz5
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add mz5 datatype
2017-08-25 18:42:14 +02:00
Dannon Baker
cf897795fe
Merge pull request #4496 from guerler/fix_drag_drop_firefox
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[17.05] Fix drag and drop from history for Firefox
2017-08-25 12:41:39 -04:00
E Rasche
cd6cc88ac1
Plain theme
2017-08-25 16:41:15 +00:00
E Rasche
68f9c6905e
Large click target for tools
2017-08-25 16:40:49 +00:00
E Rasche
2ff4292cd6
move to somewhere it can be overridden
2017-08-25 16:40:49 +00:00
guerler
3ef39b390c
Fix drag and drop from history for firefox
2017-08-25 12:09:34 -04:00
Dannon Baker
df0507e494
Merge pull request #4471 from erasche/reports-sentry-dsn
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needed for sentry functionality in reports webapp
2017-08-25 06:23:34 -04:00
Eric Rasche
f09b5c5b9d
Merge pull request #19 from dannon/reports-sentry-dsn
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Fixes for reports sentry dsn (lint and missing import).
2017-08-25 10:31:06 +02:00
Dannon Baker
0e467b73bc
Fixes for reports sentry dsn (lint and missing import).
2017-08-24 21:45:16 -04:00
Dannon Baker
c89233c7cb
Merge pull request #4477 from nsoranzo/vcf_bcf_fixes
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Fixes for VCF/BCF datatypes
2017-08-24 20:28:30 -04:00
Martin Cech
1426225a78
Merge pull request #4494 from dannon/no_mobile
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Remove /mobile and associated templates
2017-08-24 19:15:39 -04:00
Dannon Baker
4c14de6955
strip jqtouch
2017-08-24 18:13:54 -04:00
Dannon Baker
e542c47872
Remove ancient 'iphone' styling that is unused (and missing assets)
2017-08-24 17:59:55 -04:00
Dannon Baker
b80ee79b43
Remove /mobile and associated templates. It has been deactivated for almost three years now.
2017-08-24 17:17:56 -04:00
Dannon Baker
5ae1446970
Merge pull request #4492 from guerler/fix_subworkflow_comma
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Remove unused comma from subworkflow populator
2017-08-24 16:22:18 -04:00
guerler
5d04c593b6
Removes unused comma from subworkflow populator
2017-08-24 14:55:37 -04:00
Dannon Baker
001d94ae4e
Merge pull request #4479 from nsoranzo/use_pysam_in_verify
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Use pysam instead of samtools binary
2017-08-24 11:45:45 -04:00
Eric Rasche
a83438159c
Merge pull request #4458 from xgaia/interactive_environment
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don't uppercase envoverride
2017-08-23 20:36:21 +02:00
Dannon Baker
89c811b790
Move 'Copy History Items' to the bottom of the second column in the old copy histories page.
2017-08-23 14:10:22 -04:00
Dannon Baker
27bd71332a
Merge pull request #4485 from martenson/remove-exclamation
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replace exclamation with a clock icon
2017-08-23 13:56:20 -04:00
Martin Cech
a6632f3133
replace exclamation with a clock icon
2017-08-23 13:26:46 -04:00
guerler
ce7d8a2fc1
Validate workflow step after step argument injection
2017-08-23 11:31:04 -04:00
Nicola Soranzo
d3ae7351f7
Use pysam instead of samtools binary
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This will make it possible to remove the requirement of having `samtools`
installed when testing tools, e.g. in the tools-iuc TravisCI setup:
https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59
2017-08-22 20:42:57 +01:00
Nicola Soranzo
a63af63b41
Add requirement for bcftools to set_metadata tool
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The `bcftools` binary is used by the `set_meta()` method of the `Bcf`
datatype class. Having a `<requirement>` for it in the set_metadata tool
makes it possible to use conda to resolve the dependency instead of
forcing the admin to install `bcftools` on the PATH of the Galaxy user.
This will also fix errors like
https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994
when running
```
planemo test --conda_dependency_resolution --conda_auto_install
```
2017-08-22 18:29:51 +01:00
Nicola Soranzo
8dc0e697d3
Fix vcf_bgzip datatype
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In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made
a proper datatype with the introduction of the `VcfGz` class, but was
still described as a subclass in `datatypes_conf.xml` .
Also fix `file_ext` attribute in `BaseVcf` and subclasses.
2017-08-22 17:53:40 +01:00
Nicola Soranzo
da5b72a030
Alias bcf_bgzip datatype to bcf. Add bcf_uncompressed and converters
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Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353
(only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip`
datatype (introduced 2 years later in
https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate.
This adds also a distinct `bcf_uncompressed` datatype (and converters) for
the rare cases when it may be useful.
2017-08-22 17:44:53 +01:00
Nicola Soranzo
63d1d428a1
Merge pull request #4469 from guerler/fix_quota_api
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Fix quota function name
2017-08-21 16:28:46 +01:00
E Rasche
ae48774f54
needed for sentry functionality in reports webapp
2017-08-21 15:21:56 +02:00
guerler
092ad6d67f
Fix quota function name
2017-08-21 08:28:25 -04:00
John Chilton
e3b3457b1f
Merge pull request #4465 from mvdbeek/workflow_invocation_security_check
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Fix checking WorkflowInvocation for published workflows
2017-08-21 07:10:08 -04:00
Martin Cech
2346c0aa7e
Merge pull request #4467 from mvdbeek/saved_history_tags
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More items per page in saved history and directly show tags
2017-08-20 23:21:18 -04:00
mvdbeek
a9d5c7c59c
Show tag if < 3 tags on history
2017-08-20 17:43:47 +02:00
mvdbeek
0e46888eed
Show up to 15 histories by default in saved histories menu
2017-08-20 17:42:18 +02:00
mvdbeek
64f8e74ade
Fix subworkflow tests
2017-08-20 12:49:43 +02:00
mvdbeek
cff306b86b
Only skip check_security checks if check_ownership and check_accessible are false
2017-08-20 11:24:09 +02:00
mvdbeek
2d16470132
Allow admin user to view workflow invocation (thx @nsoranzo)
2017-08-20 11:21:01 +02:00
Dannon Baker