 Martin Cech
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01cd002652
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data libraries: API improvements, access permissions work, started with UI for adding files from history work
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2014-04-11 17:29:36 -04:00 |
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Dannon Baker
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1bbe1b28c9
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Merged in jlhg/galaxy-central (pull request #365)
Update the job exit codes
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2014-04-11 11:33:20 -04:00 |
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Jian-Long Huang
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fbdf57aa63
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Update the job exit codes
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2014-04-11 21:41:39 +08:00 |
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Nicola Soranzo
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46641daaa7
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Merge galaxy/galaxy-central default branch.
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2014-04-11 12:00:39 +02:00 |
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Jeremy Goecks
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80b603902a
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Merge next-stable branch to default.
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2014-04-10 17:21:38 -04:00 |
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Jeremy Goecks
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28ddf4bcc2
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Updates to Sweepster to get it working again.
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2014-04-10 17:21:00 -04:00 |
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Greg Von Kuster
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8bce650dda
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Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
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2014-04-10 17:11:01 -04:00 |
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Daniel Blankenberg
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34f9066503
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merge next-stable
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2014-04-10 16:48:31 -04:00 |
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Daniel Blankenberg
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c5f3f75ad5
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Fix for route used in displaying images on tool installed from a toolshed.
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2014-04-10 16:48:07 -04:00 |
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Martin Cech
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6854dbd523
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history API: allow anon users import public datasets into their (only) history, add exception for unknown datatype
library API: don't show folders without single accesible item to anonyms
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2014-04-10 16:45:59 -04:00 |
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Martin Cech
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0dd3187401
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data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation
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2014-04-10 15:05:33 -04:00 |
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Nicola Soranzo
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f73d5fba6c
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Fix old wiki links.
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2014-04-10 20:00:45 +02:00 |
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Nicola Soranzo
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61c427c154
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Fix a broken import. Cleanup imports.
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2014-04-10 19:57:25 +02:00 |
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Nicola Soranzo
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d7b542d3c2
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PEP8 whitespace fixes.
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2014-04-10 19:56:43 +02:00 |
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Daniel Blankenberg
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2b52d39816
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Change suc.get_url_from_tool_shed to common_util.get_tool_shed_url_from_tool_shed_registry.
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2014-04-10 13:49:43 -04:00 |
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Daniel Blankenberg
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ed52fb0cd2
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merge next-stable
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2014-04-10 13:40:00 -04:00 |
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Daniel Blankenberg
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e83208a0c1
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When posting to BioStar include a ToolShed url, as applicable.
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2014-04-10 13:39:41 -04:00 |
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Daniel Blankenberg
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d197d2c17b
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Include tool version information in bug reports.
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2014-04-10 13:38:44 -04:00 |
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Nicola Soranzo
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54da17c1ef
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Remove unused method. Cleanup imports.
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2014-04-10 18:35:18 +02:00 |
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Nicola Soranzo
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02dae93ad0
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Remove unused method.
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2014-04-10 18:22:32 +02:00 |
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Greg Von Kuster
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b436a8082f
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Display repository dependency definition attributes for repositories being installed into Galaxy where the dependency hierarchy cannot be determined likely due to invalid dependency definitions.
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2014-04-10 11:35:37 -04:00 |
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Carl Eberhard
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86da018f62
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Metrics API: allow posting of metrics sending to app.trace_logger.log if available
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2014-04-09 16:15:00 -04:00 |
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Jeremy Goecks
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be37a0846c
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Automated merge of next-stable to default.
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2014-04-09 12:53:57 -04:00 |
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Jeremy Goecks
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38452da57a
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SAM/BAM data provider: fix bug and streamline code to support both genomes with reference data and those without.
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2014-04-09 12:53:34 -04:00 |
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Jeremy Goecks
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c892a67f13
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Genome data provider: (a) handle regions with no mapped reads and (b) clean up trailing whitespace.
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2014-04-09 10:47:22 -04:00 |
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Greg Von Kuster
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27e60943bf
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The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
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2014-04-09 10:11:48 -04:00 |
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Carl Eberhard
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5120673dbd
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Metrics: allow time to be passed into fluent_log.py, log
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2014-04-08 12:55:30 -04:00 |
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Carl Eberhard
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b5b2635b0a
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Fix encoding/serialization of returned data from HDA create API
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2014-04-07 10:10:26 -04:00 |
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Greg Von Kuster
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a5161f2c7d
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Enhance error message displayed when installing a repository into Galaxy that has an invalid repository dependency definiton.
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2014-04-04 11:55:24 -04:00 |
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Daniel Blankenberg
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5845ca36a3
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Provide a full URL including protocol in activation emails.
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2014-04-04 11:46:03 -04:00 |
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Greg Von Kuster
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2abe24b292
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Better fix than ea1fbe9 and handle first discovered unhandled secure / insecure protocol issue when messing with the tool shed url for installed repositories.
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2014-04-03 17:40:44 -04:00 |
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Greg Von Kuster
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9f5f3a93e1
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Add exception handling when updating an installed repository to a revision that include newly defined dependency definitions.
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2014-04-03 12:00:25 -04:00 |
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Daniel Blankenberg
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a5b23557bf
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Change Biostar 'submit' parameter to be called 'action'. Resolves needing to use workaround of 'click()' on submit button instead of submit() on form.
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2014-04-03 11:17:47 -04:00 |
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Greg Von Kuster
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8f031dfd7b
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Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to "False") to the <repository> tag when a repository was exported.
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2014-04-03 10:19:46 -04:00 |
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Greg Von Kuster
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971e9d6f88
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Don't add unnecessary (and problematic) prior_installation_required attributes to repository dependency definitions when exporting a repository and its dependencies into a capsule.
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2014-04-03 09:31:43 -04:00 |
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Greg Von Kuster
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ffa19b77a5
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Add a new RepositoryGridFilterManager to the Tool Shed framework to support filtering the repositories displayed in the many Tool Shed grids. The current filters are CERTIFIED_LEVEL_ONE, CERTIFIED_LEVEL_ONE_SUITE and CERTIFIED_LEVEL_TWO, CERTIFIED_LEVEL_TWO_SUITE. The "level one" filters display repositories or suites that have been certified by the Tool Shed's install and test framework. The "level two" filters are not yet supported (the query enhancements are trivial, but not yet done) since no repositories in the test or main Tool Shed have been certified at this level (this level requires reviews and approvals by IUC members). When set, filters are stored in session cookies. Filters are easy to set. The Javascript event handler (e.g. checking a filter checkbox) would make a call something like: trans.app.repository_grid_filter_manager.set_filter( trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE ).
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2014-04-02 15:18:40 -04:00 |
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Dave Bouvier
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0994d4c2bd
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Fix issue in migrations where the same complex repository would be installed once for each repository that depends on it.
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2014-04-02 09:13:33 -04:00 |
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Greg Von Kuster
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7e9f07c9d3
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Don't require categories and status attributes to be associated with a repository being imported from a capsule, although they should always exist.
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2014-04-02 07:22:01 -04:00 |
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Dave Bouvier
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f807d8f406
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Remove escaped double quotes from setup_virtualenv action.
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2014-04-01 14:48:48 -04:00 |
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Jeremy Goecks
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67288cb54f
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Fix for 615d504: do not use downsampling when all reads can be returned.
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2014-04-01 14:45:34 -04:00 |
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Daniel Blankenberg
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01a77cc319
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Update Biostar question posting to use POST. Have biostar bug reports automatically post.
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2014-04-01 14:11:56 -04:00 |
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Dave Bouvier
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10cda06773
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Pass shell=True to subprocess.Popen, which eliminates the need to escape double quotes and prepend /bin/sh -c to a tool dependency shell command.
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2014-04-01 13:08:02 -04:00 |
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Dave Bouvier
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83af05b1f2
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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
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2014-04-01 11:04:32 -04:00 |
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Jeremy Goecks
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75d9496e10
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Genome data providers: (a) organize imports and (b) implement random and nth read iterators to downsample deep coverage regions. Use nth read iterator by default because it is the fastest.
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2014-04-01 10:30:12 -04:00 |
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Martin Cech
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a1e9cf6f07
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data libraries, don't allow showing deleted libraries to non-admins; provide information what actions user is allowed to do on library;
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2014-03-31 15:36:49 -04:00 |
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Dannon Baker
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d10be6b718
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Merged in nsoranzo/galaxy-central (pull request #355)
Workflow API: show also workflow owner, so a user can check it before importing.
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2014-03-31 13:21:49 -04:00 |
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Martin Cech
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14760aba92
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added is_admin to the javascript user object for UI rendering purposes;
modified is_admin_user in masthead config to be consistent with standard is_admin check
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2014-03-31 12:55:06 -04:00 |
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Greg Von Kuster
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8254c7a62c
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Eliminate unused method in the tool shed's repository controller.
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2014-03-31 08:00:19 -04:00 |
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Greg Von Kuster
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45ec91d466
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Improvements for populating the tool panel when installing a repository containing a version of a tool alreadly loaded in the tool panel.
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2014-03-31 07:37:45 -04:00 |
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Greg Von Kuster
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8420fc65cd
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When multiple versions of the same tool are loaded into the Galaxy tool panel, make sure the newest version of the tool is displayed by default in the tool version select list on the tool form when it is initially loaded.
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2014-03-30 22:48:17 -04:00 |
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