John Chilton
762337e110
Fix import orders for updates to flake8_import_order.
2016-10-17 11:54:56 -04:00
Martin Cech
a895c823da
Merge pull request #3019 from blankenberg/collection-wf-resume-error
...
Fix for rerunning tool with workflow resume that is part of a collection.
2016-10-14 10:38:37 -04:00
Dannon Baker
28bb83f0ab
Merge pull request #3055 from dannon/cherrypick_masthead_fix
...
Cherrypick masthead fix
2016-10-14 09:57:50 -04:00
Dannon Baker
6312d8052b
Rebuild cilent.
2016-10-14 09:43:41 -04:00
Scott Szakonyi
36134bca69
Added code to adjust top setting of tool search if messagebox is visible, issue 2907
2016-10-14 09:40:34 -04:00
Martin Cech
e5913a49e2
Merge pull request #3047 from galaxyproject/tool_tarball_fix
...
Fix downloading tool tarball with boolean test input values.
2016-10-14 09:22:03 -04:00
Nicola Soranzo
d26f46423e
Merge pull request #3042 from dannon/image_detection_fixes
...
Image detection fixes
2016-10-14 10:27:17 +01:00
Dannon Baker
4446ccc98c
Merge pull request #3045 from blankenberg/value_to_display_text-fix
...
Fix for displaying parameters to the user, that have a False value.
2016-10-13 17:54:21 -04:00
Dannon Baker
0062eacfdf
Merge pull request #3044 from blankenberg/gff-filter-tool-fix
...
Fix GFF attribute filtering tool broken in #2983
2016-10-13 14:40:03 -04:00
Dannon Baker
277727ada6
Merge pull request #3041 from nsoranzo/flake8-import-order
...
Change __all__ from list to tuple [1/2]
2016-10-13 13:50:24 -04:00
Dave B
f6d5f3c4a2
Fix downloading tool tarball with boolean test input values.
2016-10-13 12:42:54 -04:00
Dannon Baker
36ae57c6e0
Merge pull request #3043 from blankenberg/fix-filter-tool
...
Fix tabular filtering tool broken in #2983
2016-10-13 12:33:34 -04:00
Martin Cech
a22a4d0bd5
Merge pull request #3046 from erasche/remove_warning
...
Remove outdated warning on ID_SECRET
2016-10-13 12:25:25 -04:00
Eric Rasche
6c17d1a823
Remove outdated warning
...
After digging through the code I am not finding evidence that this
was ever possible to do, at least not since sometime pre-2010.
2016-10-13 16:21:12 +00:00
Dannon Baker
4bc4297768
Simplify, strip out passing of image.
2016-10-13 12:09:18 -04:00
Dannon Baker
ed263bf8a5
import order.
2016-10-13 12:07:25 -04:00
Daniel Blankenberg
b6d4473aa0
Fix for displaying parameters to the user, that have a False value.
...
Previously, e.g. an integer with a value of 0 would display "Not available.".
2016-10-13 11:19:37 -04:00
Daniel Blankenberg
32bc17cdaa
Whitespace fix
2016-10-13 11:08:18 -04:00
Daniel Blankenberg
5d294ea7d3
Fix GFF attribute filtering tool broken in #2983
2016-10-13 10:54:41 -04:00
Daniel Blankenberg
ba07956117
Fix tabular filtering tool broken in #2983
2016-10-13 10:40:40 -04:00
Dannon Baker
cb6e25278c
Refactoring, because it was bugging me.
2016-10-13 10:25:18 -04:00
Dannon Baker
bb44288968
Failthrough to using imghdr when PIL does not detect an image correctly.
...
Some misc cleanup, avoiding use of system functions as variable names,
etc.
2016-10-13 09:55:01 -04:00
Nicola Soranzo
77f78cfbc7
Change __all__ from list to tuple
...
Also fix import order and Python3 compatibility.
2016-10-13 14:05:03 +01:00
John Chilton
c6713e7c31
Merge pull request #3039 from nsoranzo/fix_for_2742
...
Fix workflow extraction API tests on PostgreSQL
2016-10-12 22:54:56 -04:00
Martin Cech
1e2688f157
Merge pull request #3024 from jmchilton/multi_optional_param
...
Add documentation on optional ``multiple="true"`` data parameters.
2016-10-12 20:05:24 -04:00
Nicola Soranzo
04bf2153b8
WorkflowSummary: add dict to map a job id to its representative job
...
Fix #2742 introduced in commit 9ede8e556b
2016-10-12 17:25:42 +01:00
Nicola Soranzo
dcde64ce40
Fix import order. Fix typos and improve readability
2016-10-12 17:25:37 +01:00
Martin Cech
58d608b906
Merge pull request #3036 from blankenberg/fix-dep-shell-order
...
Fix dependency ordering broken in #2917 .
2016-10-11 14:28:59 -04:00
Daniel Blankenberg
2b9281a378
Fix dependency ordering broken in #2917 .
...
We will store dependencies in an OrderedDict, matching the order of `<requirements>`.
Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting.
2016-10-11 13:10:50 -04:00
Nicola Soranzo
1156006733
Merge branch 'release_16.07' into dev
...
Conflicts:
lib/galaxy/tools/deps/__init__.py
2016-10-11 16:50:37 +01:00
Nicola Soranzo
3300a73c9d
Merge branch 'release_16.04' into release_16.07
2016-10-11 16:48:09 +01:00
Martin Cech
2adb98e58c
Merge pull request #3034 from mvdbeek/skip_python_install_travis
...
[16.04] Remove travis-ci python installation, since python2.7 is preinstalled…
2016-10-11 11:37:47 -04:00
Marius van den Beek
39fb030f13
Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now
2016-10-11 17:07:23 +02:00
Daniel Blankenberg
6639a181df
Merge pull request #3025 from mvdbeek/cache_fix
...
Cache fix
2016-10-11 10:18:23 -04:00
John Chilton
191bae9a2b
Merge pull request #3028 from carlfeberhard/fix.tiff
...
Datatypes: include base classes in search by name
2016-10-10 22:25:58 -04:00
John Chilton
75d1f8496a
Merge pull request #3031 from nsoranzo/flake8-import-order
...
Fix import order and Python3 compatibility for most of test/
2016-10-10 21:21:21 -04:00
John Chilton
7d642c063f
Merge pull request #3032 from martenson/link-mulled-docs
...
add muled docs to admin index
2016-10-10 21:20:51 -04:00
Martin Cech
1a2d75fade
add muled docs to admin index
2016-10-10 20:54:26 -04:00
Martin Cech
7db241faa6
Merge pull request #2986 from jmchilton/mulled
...
Implement beta support for discovering mulled containers for dependencies.
2016-10-10 20:36:00 -04:00
Martin Cech
bcabbd8707
minor changes to mulled admin docs
2016-10-10 19:26:36 -04:00
Martin Cech
20dcc4d693
remove duplicated option from config sample
2016-10-10 19:19:51 -04:00
Nicola Soranzo
1e32c0926c
Fix import order and Python3 compatibility for most of test/
2016-10-10 19:06:22 +01:00
John Chilton
f0b988da78
Bring in latest galaxy-lib fixes.
2016-10-10 11:08:45 -04:00
John Chilton
91bfecea67
Add documentation on optional `multiple="true"` data parameters.
...
Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility).
Rebased with indention requested by @nsoranzo and fixes for the test case tool.
2016-10-10 10:51:36 -04:00
carlfeberhard
fad562876f
Datatypes: include base classes in search by name
...
Fixes #2982
Adds the base class 'images.Image' to the list of classes
returnable by 'datatypes_registry.get_datatype_class_by_name'.
Normally that method searches the registry's list of datatypes and
those are instantiable classes only. The images.Image can be
considered an abstract base class and you'd never create a dataset
of that datatype.
The method is used for getting classes for 'isinstance' tests, however,
so including base classes like 'images.Image' allow testing for all
its image subclasses. This change makes that possible and allows the
method (and its consumers) to behave in a much more predictable and
useful manner.
2016-10-10 10:31:29 -04:00
Björn Grüning
ddacf38a11
Merge pull request #3023 from jmchilton/fix_abyss
...
[16.07] Fix for bioconda recipes depending on conda-forge.
2016-10-10 14:34:48 +02:00
John Chilton
4b5114bed1
Merge pull request #50 from jmchilton/mulled_docs
...
Add initial documentation about the new mulled features.
2016-10-10 07:15:16 -04:00
Björn Grüning
217854827a
Merge pull request #3027 from ramezrawas/patch-1
...
Missing double quotation
2016-10-10 10:23:37 +02:00
ramezrawas
ad0d0bc7ce
Missing double quotation
...
line 3664: name="output_vcf>
2016-10-10 09:52:02 +02:00
Björn Grüning
654b5e9322
Add initial documentation about the new mulled features.
2016-10-09 12:40:50 +02:00
John Chilton