 Carl Eberhard
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b8fb01b2cc
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(alt)history: split files up, rework names, add global Galaxy namespace
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2012-11-06 15:54:47 -05:00 |
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Carl Eberhard
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48d58a8e58
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pack scripts
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2012-11-06 14:09:40 -05:00 |
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Carl Eberhard
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88ec8035d1
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quota meter: fix multiple api calls on first history render; controllers/root.py: set up to move show_deleted/hidden into client
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2012-11-06 14:07:21 -05:00 |
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Daniel Blankenberg
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7f3e411628
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Allow rerun to access hidden datasets.
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2012-11-06 12:57:23 -05:00 |
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Richard Burhans
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5817bbe2f1
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Fixed installation of toolsheds containing proprietary datatypes
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2012-11-06 11:22:56 -05:00 |
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Jeremy Goecks
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a6fd79c548
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Circster improvements: (a) fetch a smaller amount of data on load and (b) use large quantile rather than max for top data range to limit impact of exceptionally large values.
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2012-11-06 09:52:23 -05:00 |
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Greg Von Kuster
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df6f274243
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Per James Johnson, handle files with a .tar extension when installing tool dependencies along with a tool shed repository.
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2012-11-06 08:38:52 -05:00 |
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Carl Eberhard
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b9741f77df
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(alt)history: incorporate quota meter; bugifxes
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2012-11-05 16:59:20 -05:00 |
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Carl Eberhard
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2b2bc12005
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added user backbone model; added quota meter view on user model
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2012-11-05 16:56:28 -05:00 |
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Carl Eberhard
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ec818e90c5
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api/users.show: added current as viable id to display json for trans.user; show, index: added key 'auota_percent' to json, returns null if no quota on user, percent otherwise
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2012-11-05 16:51:58 -05:00 |
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Carl Eberhard
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fffde1f49e
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api/history_contents: allow anon-user to query own, current history; improve doc string
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2012-11-05 16:49:58 -05:00 |
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Carl Eberhard
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37e475f8a0
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comments & docs for QuotaAgent.get_percent
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2012-11-05 16:47:14 -05:00 |
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Carl Eberhard
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c0532e1d66
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fix to model/__init__: was importing sys from galaxy.web.form_builder.*
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2012-11-05 16:45:10 -05:00 |
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Carl Eberhard
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6e0468721c
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util/debugging.py: add stack trace formatter
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2012-11-05 16:42:16 -05:00 |
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Dannon Baker
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e27477f1ec
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Cloud Launch: Fix non-keyboard paste detection for cluster lookup step.
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2012-11-05 15:30:44 -05:00 |
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Dannon Baker
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1dc332babe
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Security: Prevent potential reflected XSS via MessageException (possible in the case of invalid/malicious id lookups, for instance). Cleanup imports.
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2012-11-05 15:21:05 -05:00 |
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Daniel Blankenberg
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18e4d4bcf9
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Add a message about tools that will not be enabled during migration due to not being in the tool_conf.xml.
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2012-11-05 11:09:50 -05:00 |
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Jeremy Goecks
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aa2d69a4e3
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Pack scripts.
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2012-11-04 21:44:29 -05:00 |
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Jeremy Goecks
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2ee25fa5d3
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When running tools in Trackster, use Region object.
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2012-11-04 19:26:33 -05:00 |
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Jeremy Goecks
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7a0ce2c94f
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Transition track labels when adding/removing tracks.
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2012-11-04 14:49:46 -05:00 |
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Jeremy Goecks
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9e567df17b
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Unordered GTF parsing enhancements: (a) make more lenient by default so that transcript_ids are local to chromosomes, as is the case for some popular data sources and (b) add 'strict' mode for strict parsing.
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2012-11-04 11:04:55 -05:00 |
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Scott McManus
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efd099f4a1
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The input datatype for display changed from LibraryDataset to Dataset, causing permission-checking issues. They've been fixed.
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2012-11-04 01:49:43 -05:00 |
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Dave Clements
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f39c2cb970
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Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.*
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2012-10-31 15:41:13 -07:00 |
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Jeremy Goecks
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f4db9b8be4
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Circster: (a) create mixin for drawing tick labels and (b) use ticks for denoting chromosome length and track min/max.
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2012-11-02 16:15:15 -04:00 |
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Scott McManus
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7f07840a89
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Temporarily reverted library browsing.
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2012-11-02 15:38:54 -04:00 |
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Dannon Baker
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c41e8923b8
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Cloudlaunch: Automatically detect placement AZ of volumes from existing clusters, and launch using those placements. This prevents any "CRITICAL: This instance must be relaunched in zone..." at cloudman start. Also reworked error handling.
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2012-11-01 15:39:38 -04:00 |
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Jeremy Goecks
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3d491f63c1
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Pack scripts.
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2012-11-01 13:27:07 -04:00 |
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Jeremy Goecks
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49847e35c2
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Provide option to retry dataset indexing/conversion in Trackster. Also, move is_true method into Web helpers for general access.
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2012-11-01 10:04:12 -04:00 |
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Jeremy Goecks
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147d6c94e0
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Viz framework: (a) add option to store open file reference in data providers rather than recreating each time and (b) add ticks marks in Circster for chromosome lengths.
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2012-10-31 17:51:38 -04:00 |
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Jeremy Goecks
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aa7eee99b1
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Fix bug in getting dataset id in 63f3b08
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2012-10-31 15:58:28 -04:00 |
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Carl Eberhard
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0adb4444e8
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api/history_contents: (1) index: if passed ids=<id|csv id list> in query string, provide full data (as history_contents.show) for each id listed (if no 'ids' - use previous summary behaviour), return error string; (2) show: return 'accessible', 'api_type' (consistent with summary style in index), 'display_types', 'display_apps', 'file_ext', 'hid', 'history_id', 'meta_files' (file types of associated files for generating download urls, eg. myBam.meta_files: [{ 'file_type' : 'bam_index' }]), 'visualizations' (list of visualization names appr. for this hda), 'peek' (data.peek as used in the history panel), return error string;
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2012-10-30 16:55:23 -04:00 |
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Carl Eberhard
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2eb951587d
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api/histories.show: add 'nice_size', 'annotation', 'state_ids' (map of possible hda states : lists of hda ids in those states ), reorder history state from child hda states (running/queued higher priority than error), return error string;
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2012-10-30 16:53:10 -04:00 |
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Carl Eberhard
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1dda62a051
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galaxy/exceptions: add __str__ to MessageException; galaxy/model: add hda.purged to hda.get_api_value
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2012-10-30 16:50:37 -04:00 |
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Carl Eberhard
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29a6f731f4
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controller/UsesHistoryDatasetAssociation: get_dataset: allow encoded ids; get_dataset, get_history_dataset_association: add check_state param: check hda.state == 'UPLOADING' to allow api fetch on uploading files, (should be backwards compat with existing calls)
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2012-10-30 16:46:55 -04:00 |
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Carl Eberhard
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8e6ebda032
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pack scripts
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2012-10-30 16:42:11 -04:00 |
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Carl Eberhard
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320706f329
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history.js: add hda updater, pull model data from common api code (in initial mako render, and on fetch/update), set up url templates for history, hda models
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2012-10-30 16:39:47 -04:00 |
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Jeremy Goecks
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f2658d4d77
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Data providers: (a) add option to report interchromosomal interactions and (b) pass kwargs to get_iterator method for filtering purposes.
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2012-10-30 15:15:11 -04:00 |
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Dannon Baker
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7cff192229
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Tabular Display: left-align 'list' column type.
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2012-10-30 15:08:59 -04:00 |
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Daniel Blankenberg
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f7d92d566b
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When migrating tools, if install_dependencies is True, but tool_dependency_dir is not set, do not attempt to install, but print informative error message.
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2012-10-30 14:46:12 -04:00 |
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Jeremy Goecks
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7b19a84ba8
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UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b) remove version information from jQuery UI file names; (c) add generic jQueryUI search+select combobox widget; (d) use combobox widget for choosing dbkey in Trackster visualizations. Also pack scripts.
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2012-10-30 09:07:29 -04:00 |
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Jeremy Goecks
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28a97c62b1
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GFF/GTF reading and visualization enhancements: (a) enable GFF to FLI conversion and (b) better feature aggregation.
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2012-10-29 10:44:32 -04:00 |
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James Taylor
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56f99bbb99
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libraries: fix in query for 'datasets_are_public'
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2012-10-26 16:23:01 -04:00 |
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Greg Von Kuster
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ea3c9c66e5
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Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps.
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2012-10-26 15:39:50 -04:00 |
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Nate Coraor
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4421e1bbd1
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Download eggs from Galaxy resources in EC2.
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2012-10-26 12:56:23 -04:00 |
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Nate Coraor
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6e6b6048f4
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Log the underlying cause of job output collection failure in the drmaa runner.
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2012-10-26 10:55:46 -04:00 |
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Ross Lazarus
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acd5a48bfb
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Revert use_header_names to default false - breaks a couple of existing tests - would need to repair those too.
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2012-10-26 16:03:10 +11:00 |
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Ross Lazarus
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6a892b3555
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Fix parameters for fastqc to work properly with bam and with a contaminants file
Been b0rken for a long time - probably not much used..
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2012-10-26 16:00:13 +11:00 |
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Greg Von Kuster
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b73bd9f834
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Fix for determining the extraction directory for tool dependency tarballs when installing tool dependencies along with tool shed repositories.
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2012-10-25 14:46:57 -04:00 |
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Dannon Baker
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63125fcdd1
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Pack workflow editor javascript to be compatible with changes in pull request #76
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2012-10-25 10:52:26 -07:00 |
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Dave Bouvier
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cc608c31b2
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Updated migration script to reference repository with correct use of tool dependency tag sets.
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2012-10-25 13:25:39 -04:00 |
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