John Chilton
932b8f59ec
Merge pull request #4250 from bwlang/spelling_style_fixes
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Spacing convention, -> util.asbool, atribute -> attribute
2017-07-05 07:11:15 -04:00
John Chilton
ac59d1d6e0
Merge pull request #4259 from gregvonkuster/ptkscmp
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Add ptkscmp datatype
2017-07-04 05:33:32 -04:00
John Chilton
666c4bcbb0
Merge remote-tracking branch 'guerler/fix_shared_history' into dev
2017-07-03 20:46:42 -04:00
John Chilton
bc8d6dd1da
Merge pull request #4271 from mvdbeek/job_rerun_changed_parameters
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Keep tool parameters when rerunning a job
2017-07-03 20:37:00 -04:00
mvdbeek
3d16aa62fa
Also remove the inner try/except
2017-07-03 13:25:35 +02:00
mvdbeek
e379f44eff
Remove outer try/except in Eland sniffer
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Exceptions in a sniffer are already caught in
galaxy.datatypes.sniff.guess_ext() and are equivalent to `return False`.
Thanks @nsoranzo!
2017-07-03 13:25:35 +02:00
mvdbeek
65e3365948
Simplify if/elif (thx @nsoranzo)
2017-07-02 15:49:32 +02:00
mvdbeek
36bdd99fbc
Keep tool parameters when rerunning a job
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with a different tool version, as long as the parameter did not change.
Addresses https://github.com/galaxyproject/galaxy/issues/1729
2017-06-30 16:54:45 +02:00
mvdbeek
cbcee585b5
Use contextmanager when using compression_util.get_fileobj()
2017-06-30 11:56:59 +02:00
guerler
fb73b5dc14
Align operation handling
2017-06-29 04:03:30 +02:00
guerler
5de92dfbf4
Restore basic copy and unshare operations
2017-06-29 04:01:29 +02:00
guerler
f8c2c0b035
Add shared history grid to client
2017-06-29 03:47:46 +02:00
Dannon Baker
8169129981
Merge pull request #4253 from bwlang/refactor_tag_manager
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refactors tag manager to use only what it needs…
2017-06-28 11:40:32 -04:00
Greg Von Kuster
66dabf65ab
Add ptkscmp datatype for PlantTribes significant components in the Ks distribution
2017-06-28 10:59:11 -04:00
Brad Langhorst
8f416951bf
TagManager in toolshed is not related
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To GalaxyTagManager
Fixes toolshed failing test
2017-06-28 08:15:38 +02:00
Nicola Soranzo
40cd2df06b
Merge pull request #4239 from dpryan79/sniffSkipComments
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Enable skipping comment lines while sniffing files
2017-06-28 08:15:03 +02:00
Devon Ryan
e5e83833d1
Style and ignore '' comment_designators
2017-06-28 07:19:16 +02:00
Marius van den Beek
6cd026bc7b
Merge pull request #4237 from dpryan79/fastqSniffer_implement3571
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Sniff fastqsanger and prefer it over fastq if the quality scores match
2017-06-28 00:34:08 +02:00
Devon Ryan
e6278a778d
Remove camel case
2017-06-28 00:27:44 +02:00
Brad Langhorst
49ccf2f49c
Should address too much indentation flake issue
2017-06-27 23:30:20 +02:00
Brad Langhorst
7c86c5480b
refactors tag manager to use only what it needs…
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an sql_alchemy session, not the full app.
This makes it possible to use the tag manager from
the model.
2017-06-27 18:32:34 +02:00
Brad Langhorst
bcdb8fcbe7
Spacing convention, -> util.asbool, atribute -> attribute
2017-06-27 16:32:15 +02:00
Devon Ryan
e21e9ec15f
Ugh, there were multiple places where the sniffing order was specified (binary formats are different).
2017-06-27 15:21:34 +02:00
Nate Coraor
153b8d4dca
Merge pull request #4096 from bernt-matthias/dev
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get real user name from username and email (for submission as real user with drmaa)
2017-06-27 13:54:22 +02:00
Devon Ryan
3bb3ecb09b
Typo
2017-06-27 11:31:35 +02:00
Devon Ryan
907bd53776
Make the phred range stricter and more explicit.
2017-06-27 11:11:19 +02:00
Devon Ryan
f3853a0956
Test a non-fastqsanger file and ensure it doesn't pass the sniff test.
2017-06-27 11:01:46 +02:00
Devon Ryan
9c10b6ce5d
For file sniffing, allow get_headers() to skip comment lines, which should prevent at least some instances of #3148 .
2017-06-27 10:53:31 +02:00
Devon Ryan
8eaede3110
Fix sequence.py unit test
2017-06-27 10:11:30 +02:00
Devon Ryan
798b73eb68
Fix line reordering
2017-06-27 09:46:05 +02:00
Devon Ryan
ab1127334f
Remove debugging stuff, since everything works inside of docker
2017-06-27 09:44:39 +02:00
Nicola Soranzo
a57b4c1715
Merge branch 'release_17.05' into dev
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Conflicts:
static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js
2017-06-27 03:25:44 +02:00
Devon Ryan
bc13a16f83
Add the compressed datatypes to the sniffer lsit
2017-06-26 22:18:38 +02:00
Devon Ryan
0a942d79a3
Checking the quality lines will make fastqsanger checks rather more relevant.
2017-06-26 16:36:17 +02:00
Devon Ryan
694d8c8555
Sniff FastqSanger before Fastq, in the former case checking the quality scores for compatibility
2017-06-26 13:55:12 +02:00
Nicola Soranzo
e8c2313640
Small fixes
2017-06-26 01:30:48 +01:00
Nicola Soranzo
02ffcd5c8f
Fix import order and Python3 compatibility for lib/galaxy/datatypes/registry.py
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xref. https://github.com/galaxyproject/galaxy/issues/1715
2017-06-26 01:30:44 +01:00
Nicola Soranzo
0bfa1df72f
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
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Without this fix, the Cheetah expression:
$dataset.is_of_type('unknown_ext')
in a tool command would be equivalent to:
$dataset.is_of_type('txt')
meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.
xref. https://github.com/galaxyproject/tools-iuc/issues/1373
Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
2017-06-26 00:43:41 +01:00
Dannon Baker
a910763cd8
Merge pull request #4208 from jmchilton/singularity_volume_fix_2
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Add missing lines for fixing Singularity volumes.
2017-06-22 18:01:06 -04:00
guerler
bf65490a14
Merge branch 'dev' into grids_published
2017-06-21 12:37:15 -04:00
Dannon Baker
9b9e2aa227
Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev
2017-06-20 21:22:28 -04:00
Dannon Baker
6a0401e08e
Merge pull request #4167 from guerler/grid_histories
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Remove histories grid mako
2017-06-20 13:24:47 -04:00
John Chilton
67b798f383
Add missing lines for fixing Singularity volumes.
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These should have been included in https://github.com/galaxyproject/galaxy/pull/4180 .
2017-06-20 09:43:50 -04:00
anuprulez
8a09836ba7
Merging with dev
2017-06-19 23:10:14 +02:00
John Chilton
ea1cf742f0
Bring in Singularity fixes from galaxy-lib.
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xref https://github.com/galaxyproject/galaxy-lib/pull/67
2017-06-19 13:41:40 -04:00
John Chilton
76c6b6f5ba
Fix mulled Docker resolution.
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I broke a bunch of Docker stuff when I abstracted it out for Singularity - things like ignoring namespaces because Singularity doesn't use that concept.
Also fetching mulled-v2 images from quay.io was broken - I didn't notice this because previously there were no published images mulit-container images.
2017-06-19 13:40:33 -04:00
Matthias Bernt
698075c3d7
Merge remote-tracking branch 'upstream/dev' into dev
2017-06-19 10:40:55 +02:00
guerler
b32c1cf1a3
Check name export in legacy export section
2017-06-16 11:44:17 -04:00
guerler
90d6262ef9
Published workflows
2017-06-16 10:21:36 -04:00
guerler
3f29f13d3b
Visualizations grid
2017-06-16 09:52:15 -04:00
John Chilton