opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 10:24:38 +08:00
Code Issues Packages Projects Releases Wiki Activity
28,394 Commits 62 Branches 243 Tags
3bb3ecb09bb0ac77668d08cb1d5ecc0b7d61fa29
Commit Graph
28394 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Devon Ryan 3bb3ecb09b Typo 2017-06-27 11:31:35 +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
Nicola Soranzo a57b4c1715 Merge branch 'release_17.05' into dev 
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
Björn Grüning 46dbf8d10c Merge pull request #3076 from peterjc/gff3_filter_by_attribute 
GFF3 support in filter by attribute
 2017-06-26 18:00:45 +02:00
Nicola Soranzo ce1316d680 Merge pull request #4226 from dpryan79/CompressedFastqLines_implement4144 
Running a word count on a compressed fastq file now runs wc on the un…
 2017-06-26 14:06:26 +02:00
Devon Ryan 8a6ef05858 Single quote file names 2017-06-26 13:56:56 +02:00
peterjc 005f3d9f98 Defensive code in case standard GFF fields missing 2017-06-26 11:16:14 +01:00
peterjc c87e0eedb7 Cope with GFF3 as well as legacy GFF. 
In GFF3 have key=value rather than space separated
as in legacy GFF and GTF format. Closes #3068.
 2017-06-26 11:16:06 +01:00
peterjc cb40b01db8 Ignore blank lines and comments in GFF files 
Previously would wrongly issue warnings about valid # lines.
Closes #3067
 2017-06-26 11:15:08 +01:00
Devon Ryan 4ee1848992 Running a word count on a compressed fastq file now runs wc on the uncompressed file 2017-06-26 12:03:57 +02:00
John Chilton 3ec2c7831d Merge pull request #4224 from nsoranzo/fix_get_datatype_by_extension 
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
 2017-06-26 04:26:47 +00:00
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 
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 
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
Björn Grüning 73faf7c8b6 Merge pull request #4223 from pvanheus/patch-3 
Correct name of neo4j datatype class
 2017-06-24 05:44:38 +02:00
pvanheus 00928743bf Correct name of neo4j datatype class 
Its neo4j.Neo4jDB: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/neo4j.py#L89
 2017-06-23 23:25:09 +02:00
Dannon Baker a910763cd8 Merge pull request #4208 from jmchilton/singularity_volume_fix_2 
Add missing lines for fixing Singularity volumes.
 2017-06-22 18:01:06 -04:00
Dannon Baker c18479b79c Merge remote-tracking branch 'guerler/grids_published' into dev 2017-06-22 17:15:50 -04:00
John Chilton 27e843bfc1 Merge pull request #4213 from bgruening/improve_search_plugin 
Improve search plugin
 2017-06-22 15:49:00 -04:00
John Chilton 739fb083f0 Merge pull request #4216 from thobalose/neo4j-ie 
Upgrading Neo4j IE to 3.1
 2017-06-22 15:47:14 -04:00
Martin Cech 9dca211e2f Merge pull request #4214 from guerler/revise_tool_url 
[17.05] Improve resilience of tool url building
 2017-06-22 14:06:52 -04:00
Martin Cech 9cec283b5a make the overlay icon toggleable, change wording 2017-06-22 11:28:32 -04:00
Thoba Lose 009f44c25f using sanbi-sa image. 2017-06-22 15:00:03 +02:00
guerler a498390bef Fix basic version changes for reloaded tools 2017-06-21 23:06:15 -04:00
guerler 69e76f98fa Remove redundancy of tool_id parameter 2017-06-21 17:10:52 -04:00
Thoba Lose 3461b26540 Merge branch 'dev' of github.com:galaxyproject/galaxy into neo4j-ie 2017-06-21 21:19:37 +02:00
guerler 268ee7f1b7 Improve resilience of tool url building 2017-06-21 14:52:56 -04:00
guerler bf65490a14 Merge branch 'dev' into grids_published 2017-06-21 12:37:15 -04:00
anuprulez e9b132bd53 Merging with dev 2017-06-21 17:26:48 +02:00
anuprulez 6704872cd9 Moving the creation of script and style tags to Utils 2017-06-21 17:18:46 +02:00
Dannon Baker ecdaa04dfd Merge pull request #4210 from guerler/fix_panel_hiding 
Fix left/right panel hiding
 2017-06-21 08:38:57 -04:00
guerler 490d738ba4 Fix left/right panel hiding 2017-06-20 22:26:03 -04:00
Dannon Baker 9b9e2aa227 Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev 2017-06-20 21:22:28 -04:00
anuprulez 19231b73f3 Reduce opening of search overlay to one step - just click on the magnifier 2017-06-20 19:33:49 +02:00
Dannon Baker 6a0401e08e Merge pull request #4167 from guerler/grid_histories 
Remove histories grid mako
 2017-06-20 13:24:47 -04:00
John Chilton 67b798f383 Add missing lines for fixing Singularity volumes. 
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
anuprulez 837a5c85fc Merging changes with static files 2017-06-19 22:59:57 +02:00
Björn Grüning f4e4c08bab Merge pull request #36 from guerler/fix_cleanup 
Fixes deferred removal of previous views, augments center panel handling
 2017-06-19 22:47:40 +02:00
guerler d031758d73 Pack scripts 2017-06-19 16:08:23 -04:00
guerler 71498cabfd Fix log statement 2017-06-19 16:07:32 -04:00
guerler 21312138a4 Fix deferred form destructor 2017-06-19 16:06:58 -04:00
guerler 2c4c7147e0 Revise and fix resize handler 2017-06-19 15:48:30 -04:00
guerler 659c039601 Revise panel/iframe handling, align naming, rely on empty to trigger removal of previous view 
Repack

Move inline styles, use consistent naming
 2017-06-19 15:48:28 -04:00
Björn Grüning 89851e4c71 Merge pull request #4207 from jmchilton/mulled_container_fixes 
Various mulled container fixes.
 2017-06-19 20:45:40 +02:00
John Chilton f7ba729510 Merge pull request #4203 from guerler/fix_name_export 
[17.05] Check name type in legacy export section
 2017-06-19 14:42:56 -04:00
John Chilton ea1cf742f0 Bring in Singularity fixes from galaxy-lib. 
xref https://github.com/galaxyproject/galaxy-lib/pull/67
 2017-06-19 13:41:40 -04:00
John Chilton 76c6b6f5ba Fix mulled Docker resolution. 
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
Nicola Soranzo 2a5dc90003 Merge pull request #4199 from FredericBGA/library_upload_dir 
Debug of script library_upload_dir.py
 2017-06-16 18:52:17 +01:00
guerler b32c1cf1a3 Check name export in legacy export section 2017-06-16 11:44:17 -04:00