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2139 Commits
Author SHA1 Message Date
thobalose a1f7634fd7 Updated volume kwds. 2018-10-10 18:28:39 -04:00
Nicola Soranzo e0c269291a Merge branch 'release_18.01' into release_18.05 2018-06-23 00:04:32 +01:00
mvdbeek 5f24794efd Add basic .bai datatype 2018-06-22 19:50:43 +02:00
Dannon Baker fa2b6baef7 Revert "Remove bam to bai converter" 
This reverts commit 7e2727bc0a.
 2018-06-22 13:22:51 -04:00
guerler b0212ff45c Add phylip for msa viewer 2018-06-19 17:23:52 -04:00
guerler f6888a32d6 Add fasta datatype to msa viewer 2018-06-19 14:14:44 -04:00
Sebastian Kapust 3c36bec290 Fix tool search overlay link 2018-06-08 13:24:50 -04:00
Dannon Baker ae546cef79 Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-05-25 10:21:54 -04:00
Nate Coraor 221d92f681 Don't use the notebook URL itself for keepalive checks 2018-05-24 15:03:04 -04:00
Ubuntu 872dbfb3c4 adding idat 2018-05-21 10:18:31 +00:00
Dannon Baker c6ce1342df More standard spacing in additional config comments just added. 2018-05-18 11:41:21 +01:00
Dannon Baker 6a30fe14f1 Config rebuild 2018-05-18 11:41:08 +01:00
Martin Cech fe37996de3 rename the config option to enable_gdpr_beta 
to reflect the information that we do not guarantee compliance
 2018-05-16 12:38:46 -05:00
Martin Cech 3a9a46f772 Merge pull request #6069 from erasche/gdpr 
[18.05] GDPR Compliance Mode
 2018-05-15 20:40:20 -05:00
Helena Rasche 2f351bf3a7 rebuild configuratoin 2018-05-14 15:33:34 +02:00
Helena Rasche ee985e6bbc Update documentation 2018-05-14 11:51:10 +02:00
Helena Rasche b4bd972b71 update documentation 2018-05-10 17:44:11 +02:00
John Chilton 9bc73824a5 [18.05] Fix matches_any() checks for dynamic compressed types. 
See huge conversation on #6093.
 2018-05-10 09:47:53 -04:00
guerler e11da5fba9 Fix jqplot: boxplot, histogram 
Fix heatmap clustering

Fix nvd3 tool based types

Remove global d3 object from heatmap and jqplot
 2018-05-02 18:42:11 -04:00
Nicola Soranzo 7ce49394c3 Merge branch 'release_18.01' into release_18.05 2018-04-26 19:05:38 +01:00
Nicola Soranzo a3e6963666 Merge branch 'release_17.09' into release_18.01 2018-04-26 19:01:48 +01:00
Nicola Soranzo 7d81d2cfcb Fix 2 typos in the docs 2018-04-26 10:23:14 +01:00
Nicola Soranzo c41c84eec6 Merge branch 'release_18.01' into release_18.05 2018-04-25 18:36:11 +01:00
Nate Coraor e58034b987 Correct examples in dynamic job conf doc, remove handlers section from 
basic sample job config (defining a single default handler is no longer
needed). Fixes #5976.
 2018-04-25 13:10:04 -04:00
mvdbeek 383eb0d273 Add apply rules tool to standard tool xml sample 2018-04-24 11:10:49 -04:00
John Chilton 8af243c176 Allow rule based operations on existing collections. 
Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions.

For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules".

This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions.

This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running.
 2018-04-24 11:10:43 -04:00
John Chilton 33a28b8b8b Merge pull request #5761 from phnmnl/galaxy-prs/k8s-improves-job-handling-existing-jobs 
Kubernetes: Improves handling of existing jobs on Galaxy restart.
 2018-04-20 07:21:24 -04:00
Martin Cech 379714e5be remove sniffers that no longer exist from sample config 2018-04-19 14:16:11 -04:00
John Chilton fce2dd3ae8 Eliminate compressed datatype boiler plate. 
Just annotate auto_compressed_types="gz|bz2|gz,bz2" in datatypes_conf.xml and get for free:

- The compressed datatype with correct extension, no need to have a class definition.
- Converters from the compressed datatype to the uncompressed datatype.
- A sniffer in the correct order.

Additionally, the hacky way we were controlling whether types would be sniffed or not has been improved. This can now be set in the datatypes_conf.xml file or read from a global Galaxy configuration option for options that haven't been explicitly set on a per-datatype basis in the configuration (sniff_compressed_dynamic_datatypes_default).

This should simplify all future datatypes moving in this direction and introduces the possibility of also just loading them in dynamically as needed based on what the tools in the tool panel annotate for inputs and outputs. See a tool with an input of type "genbank.gz" should be enough to trigger this someday I hope.
 2018-04-19 14:10:33 -04:00
John Chilton 2829a1f164 Merge pull request #5854 from natefoo/run-scripts-conda 
Improve startup interoperability with Conda
 2018-04-18 16:08:13 -04:00
John Chilton 8baea1f7c7 Merge remote-tracking branch 'jmchilton/dev' into singlecellobject 2018-04-18 15:59:17 -04:00
John Chilton 921fde4b8c Merge pull request #5861 from natefoo/containers-docker-lib 
Implement the API version of the Docker containers interface
 2018-04-18 15:32:47 -04:00
Dannon 3922065d8a Merge pull request #5902 from guerler/add_logo_hivtrace 
Add proxy, logo and example file for hivtrace
 2018-04-17 18:40:18 -04:00
guerler 767a456544 Fix proxy, add logo and example file to repo for hivtrace 
Delete example file
 2018-04-17 16:37:56 -04:00
Martin Cech 5d82c1a09f Merge pull request #5807 from dannon/bs4 
Bootstrap 4 !!!!
 2018-04-17 15:21:05 -04:00
Dannon 8ed3854f07 Merge pull request #5869 from veg/dev 
HIV-TRACE visualization plug-in
 2018-04-17 12:18:06 -04:00
Pablo Moreno dc563eae75 Adds timeout behaviour for k8s existing job deletion 2018-04-15 13:49:37 +01:00
Mehmet Tekman d5cb6f636b renamed type 2018-04-14 00:04:53 +02:00
Mehmet Tekman d31c05a67d removed sniffers, removed pinned, removed classes 2018-04-13 11:27:12 +02:00
Dannon Baker bc7da96bb6 Merge remote-tracking branch 'upstream/dev' into bs4 2018-04-12 12:15:19 -04:00
Nate Coraor 91a25d0a08 Support manager failover for Docker Swarm mode 2018-04-10 12:35:26 -04:00
E Rasche 4a6eb37b47 Add config option 2018-04-10 11:36:11 +02:00
Steven Weaver cea328effa adding hivtrace datatype and updating visualization to use it 2018-04-09 16:37:34 -04:00
Steven Weaver ff15eeddbc updating hivtrace plugin to use new static paths 2018-04-09 14:55:05 -04:00
Steven Weaver f1b5849f33 Merge branch 'dev' of github.com:galaxyproject/galaxy into dev 2018-04-09 14:34:44 -04:00
Dannon Baker ae8b8d9fdf Merge remote-tracking branch 'upstream/dev' into bs4 2018-04-09 09:59:46 -04:00
Nate Coraor c42d642233 Containers: 
- Improve documentation of docker API param mapping
- Improve sample containers config file
- Fix constraints
- A couple other minor bug/logging fixes
 2018-04-06 16:07:06 -04:00
vjalili 259daf1749 Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase 
# Conflicts:
#	lib/galaxy/dependencies/pinned-requirements.txt
#	lib/galaxy/dependencies/requirements.txt
 2018-04-06 11:15:27 -07:00
Dannon Baker 075abee766 Merge pull request #5810 from guerler/viz-staging-finalize 
Plugin directory staging
 2018-04-06 09:54:53 -04:00
Dannon Baker 52af42989b Fix scratchbook tour handles. This should fix one remaining selenium 
test for BS4.
 2018-04-05 21:41:03 -04:00