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Author SHA1 Message Date
John Chilton 932b8f59ec Merge pull request #4250 from bwlang/spelling_style_fixes 
Spacing convention, -> util.asbool, atribute -> attribute
 2017-07-05 07:11:15 -04:00
John Chilton 7ce50a8ff7 Merge remote-tracking branch 'upstream/dev' into login_only 2017-07-04 05:40:31 -04:00
John Chilton ac59d1d6e0 Merge pull request #4259 from gregvonkuster/ptkscmp 
Add ptkscmp datatype
 2017-07-04 05:33:32 -04:00
Jelle Scholtalbers 010beb8270 code optimization - reuse userTab variable 2017-07-04 09:01:10 +02:00
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 
Keep tool parameters when rerunning a job
 2017-07-03 20:37:00 -04:00
Nicola Soranzo ee62fa7de8 Merge pull request #4270 from mvdbeek/context_manager_get_fileobj 
Use contextmanager when using compression_util.get_fileobj()
 2017-07-03 13:23:21 +01:00
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 
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 b928236cfa Fix indentation 2017-07-02 16:27:28 +02:00
mvdbeek 4c68e29a81 Use if/else if to determine the job_id 2017-07-02 16:24:29 +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 
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 d694b60613 Remove shared grids mako 2017-06-29 04:06:44 +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 
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
Anton Nekrutenko dd0336e7d2 Merge pull request #4113 from erasche/security-policy 
[PROCEDURES] Security policy
 2017-06-28 14:36:06 +02:00
Jelle Scholtalbers 9af36bd13b change 'register or login' to just 'login' if 'allow_user_creation=False' 2017-06-28 13:49:19 +02:00
Brad Langhorst 8f416951bf TagManager in toolshed is not related 
To GalaxyTagManager
Fixes toolshed failing test
 2017-06-28 08:15:38 +02:00
Nicola Soranzo 40cd2df06b Merge pull request #4239 from dpryan79/sniffSkipComments 
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 
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
Martin Cech e98378160a Merge pull request #4232 from pvanheus/dev 
add public-only filter for data libraries
 2017-06-27 21:41:15 +02:00
Brad Langhorst 7c86c5480b refactors tag manager to use only what it needs… 
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 
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
Martin Cech 6a43fad892 Merge branch 'dev' into lib_exclude_restricted 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
 2017-06-27 10:49:56 +02:00
Martin Cech c41b284999 adjust logic to match the include deleted checkbox 
also make client and set default user preference
 2017-06-27 10:41:22 +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 
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
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
Peter van Heusden e63ababa79 add public-only filter for data libraries 2017-06-26 17:10:45 +02:00
Devon Ryan 0a942d79a3 Checking the quality lines will make fastqsanger checks rather more relevant. 2017-06-26 16:36:17 +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
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