 Greg Von Kuster
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19862fd03b
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Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file.
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2012-03-14 17:21:03 -04:00 |
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Jeremy Goecks
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41b9ca70d1
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Trackster: make reference track compatible with changeset 8e9d2b492c4c.
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2012-03-13 17:22:56 -04:00 |
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Jeremy Goecks
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e92cbb2222
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Trackster: prevent resizing of label and reference tracks.
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2012-03-13 17:15:46 -04:00 |
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Greg Von Kuster
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ee61c8aac0
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When uploading a tarball to a tool shed repository, eliminate as many undesired directories (.svn, .git, .hg, .cvs) and files (hgrc, .hg_archival.txt, .DS_Store) as possible from the archive before committing the contents to the repository.
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2012-03-13 16:25:15 -04:00 |
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Greg Von Kuster
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878997c54c
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Fix for rerunning a tool where the correct id / version are available.
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2012-03-12 15:30:37 -04:00 |
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Greg Von Kuster
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86e2eb8c3b
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Check potential tool config files to ensure they are text before attempting to load them in tool shed repositories, and a fix handling for tools contained in a repository that don't peoperly load into Galaxy because they are missing a required entry in the tool_data_table.conf file.
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2012-03-12 13:51:07 -04:00 |
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Jeremy Goecks
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29a921d122
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Merge.
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2012-03-12 11:59:52 -04:00 |
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Jeremy Goecks
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890d27dd31
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Update converter name to be more descriptive.
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2012-03-12 11:59:41 -04:00 |
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Jeremy Goecks
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269f30e2ee
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Another config file addition to .hgignore
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2012-03-12 11:57:52 -04:00 |
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Jeremy Goecks
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31a6e60049
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Fix feature popup functionality broken in 4a7374937251 by separating track content into tiles and overlay and using different CSS rules to manage them. Pack trackster script.
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2012-03-12 11:56:29 -04:00 |
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Greg Von Kuster
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1f75e767db
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Handle tool versions with job reruns.
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2012-03-12 10:20:56 -04:00 |
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Jeremy Goecks
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fc99e5b2ca
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Update .hgignore to include new config files, tool data, and jars.
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2012-03-11 12:06:33 -04:00 |
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Jeremy Goecks
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c426e10599
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Trackster: enable resizing of feature tracks. Added generic framework for resizing tracks.
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2012-03-11 11:47:06 -04:00 |
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Jeremy Goecks
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2ebe0eb774
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Clean up temp files.
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2012-03-09 16:11:21 -05:00 |
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Dannon Baker
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a8663bba9f
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Workflows: Add run workflow directly to the editor's menu.
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2012-03-08 14:05:40 -05:00 |
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Jeremy Goecks
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b393ea6bbe
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Trackster: bug fixes for read filtering.
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2012-03-08 12:29:13 -05:00 |
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Jeremy Goecks
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047c1bff2f
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Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.
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2012-03-08 11:09:14 -05:00 |
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Dannon Baker
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6ff2de32dc
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Merged in jmchilton/galaxy-central-preseeding/import_workflow_api_script (pull request #39)
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2012-03-08 10:09:56 -05:00 |
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John Chilton
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4bc926d9f0
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Adding script to scripts/api directory for importing workflows from
file paths.
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2012-03-08 09:03:27 -06:00 |
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Jeremy Goecks
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12c9c98b95
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Add necessary space after threads option in Cuffmerge.
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2012-03-08 08:37:20 -05:00 |
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Greg Von Kuster
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ea4db057f5
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Fix for populating the tool panel and generating the integrated_tool_panel.xml file.
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2012-03-07 13:35:34 -05:00 |
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Dannon Baker
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680a0ebbd5
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Workflows: Multiple run workflows now copy input datasets to newly created histories when used.
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2012-03-07 13:13:58 -05:00 |
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Greg Von Kuster
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7901ccf7f0
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Fix for generating ToolSectionLabels in the integrated_tool_panel.xml file.
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2012-03-06 17:15:38 -05:00 |
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Jeremy Goecks
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85e13a6170
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Editable text support: (a) use jQuery function style and (b) add support for tipsy. Trackster: add help/tipsy text when setting line track/histogram max/min. Pack scripts.
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2012-03-06 16:30:03 -05:00 |
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Daniel Blankenberg
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8cd89ba26f
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Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) when downloading exported histories.
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2012-03-06 15:43:32 -05:00 |
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Daniel Blankenberg
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9815e02e34
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Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) on downloads from a library.
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2012-03-06 15:32:46 -05:00 |
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Daniel Blankenberg
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8cddff1ae5
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Fix for 'Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION): Multiple Content-Disposition headers received.' error occuring when downloading certain datasets using Chrome browser.
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2012-03-06 15:23:56 -05:00 |
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Greg Von Kuster
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fa3fd0dd65
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Introduce a new integrated_tool_panle.xml file which is initially created by parsing all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc). After the file is created, the order of the items displayed in the tool panel is defined by integrated_tool_panel.xml. Galaxy admins can easily edit the file to change the order of items in the tool panel. After it is generated, all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc) will be used to load tools, workflows, etc, while integrated tool_panel.xml will define where they are displayed.
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2012-03-06 14:50:55 -05:00 |
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Jeremy Goecks
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853028e08f
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Trackster: manually track view redraw requests so that only one redraw is done.
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2012-03-06 11:43:53 -05:00 |
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Dannon Baker
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b3b865d031
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Run workflow: Update and clarify label selector.
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2012-03-05 15:17:41 -05:00 |
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Jeremy Goecks
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47df257ff9
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Trackster: dynamic filtering of read tracks.
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2012-03-05 15:10:31 -05:00 |
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Dannon Baker
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ed58dd93ac
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Workflow Running - Properly select only Input Dataset steps for multi-input configuration.
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2012-03-05 14:44:19 -05:00 |
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Daniel Blankenberg
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bdb532db98
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In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history.
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2012-03-05 13:25:14 -05:00 |
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Dannon Baker
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7ec78e35af
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Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.
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2012-03-05 12:00:53 -05:00 |
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Greg Von Kuster
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63fb46f9f1
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Keep empty sections in the tool panel when deactivating / uninstalling a repository with tools.
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2012-03-02 15:37:35 -05:00 |
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Jeremy Goecks
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b22c78b4ac
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Merge
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2012-03-02 14:35:57 -05:00 |
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Greg Von Kuster
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0423293a5b
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Fixes for deactivating / uninstalling a repository containing tools.
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2012-03-02 14:30:41 -05:00 |
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Jeremy Goecks
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2d16ed6bcf
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Fix custom-build UI bugs.
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2012-03-02 14:29:21 -05:00 |
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Jeremy Goecks
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4648507899
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Decode visualization dataset ids before saving them.
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2012-03-02 13:40:46 -05:00 |
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Greg Von Kuster
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abe913f81e
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Fixes for managing installed repositories.
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2012-03-02 13:33:58 -05:00 |
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Greg Von Kuster
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fc1cff34b5
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Allow installed tools to have more than 1 entry in the tool panel, and several fixes for deactivating / activating / uninstalling / reinstalling repositories.
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2012-03-01 15:04:51 -05:00 |
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Jeremy Goecks
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f1a5e8eac5
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Fix CSS bugs in displaying feature popups in embedded visualizations.
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2012-03-01 14:19:17 -05:00 |
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Jeremy Goecks
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51537e2c06
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Fix bug in embedded visualization drag-zoom.
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2012-03-01 12:19:28 -05:00 |
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Daniel Blankenberg
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1fb7388e59
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Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined.
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2012-03-01 10:11:55 -05:00 |
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Dannon Baker
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b1dd7eeaa0
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Quick fix for ftp upload unicode normalization failure.
TODO: Refactor, shouldn't happen this way.
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2012-03-01 09:31:18 -05:00 |
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Jeremy Goecks
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c008d3c069
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Merge
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2012-02-29 16:54:13 -05:00 |
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Jeremy Goecks
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4348645a44
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Pack trackster script.
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2012-02-29 16:53:53 -05:00 |
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Greg Von Kuster
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305ab08cb0
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Potential fix for the buildbot.
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2012-02-29 16:27:46 -05:00 |
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Jeremy Goecks
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9b4bb79db2
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Style updates for embedded items to reduce visual footprint.
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2012-02-29 12:53:48 -05:00 |
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Dannon Baker
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351ff6bec3
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Cloud launch basics.
TODO: Tons of help text, shift instance dns wait to page level. pkey direct download.
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2012-02-29 11:58:22 -05:00 |
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