November 2011 Archives by thread

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Starting: Tue Nov 1 08:56:11 EDT 2011
Ending: Wed Nov 30 22:51:58 EST 2011
Messages: 122

• [galaxy-commits] commit/galaxy-central: dan: Fix label for 'How to specify bad variants' in variant_recalibrator.xml   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: (a) refactor tool data functionality into TiledTrack class so that it is generally available; (b) enable VcfTracks to work with tools; and (c) more robust parameter setting. Enable Unified Genotyper to work with Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug introduced in f34a17e508e5.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove debugging statements from f34a17e508e5.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: consolidated make_html_table for tabular datatypes   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix vertical scrolling via keyboard in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix a typo in tasks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Allow administrators to impersonate other users. Useful for debugging, but be aware that this gives said administrator a full session as the user, with the ability to do anything as that user (the user does not gain the administrator's privileges, however).   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: Fix signature of slit method   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: (a) give every Drawable unique id and (b) remove unused reference to jquery.scrollTo.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bug in showing 'add datasets' button and rename update_track_icons to update_icons for clarity.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix bug I introduced when I made changes to eliminate the User Type select field if no real options exist because there are no required form definitions.   Bitbucket
• [galaxy-commits] commit/galaxy-central: guru: Added 3 tools: 1) to compute weighted average values based on interval intersections (under Regional variation), 2) to perform logistic regression (under Multiple regression), 3) to compute partial R-squared (under Multiple regression).   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Temporary work-arounds for dealing with Galaxy panels when switching from workflow UI and Galaxy UI.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Improve Cufflinks' documentation for gene annotation dataset parameters.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Use panels when adding a build from a new track browser.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for implicit dataset conversion that was broken in 1827729ed37e.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix bug introduced in 0ba260ea43c4 for displaying workflows.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Actually send error reports to the creator instead of lying and saying that we did.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Invalidate other Galaxy sessions upon password change. Thanks Bob Harris!   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Squash SAMTools stderr chatter when using FreeBayes which would cause error state. FreeBayes should be updated to e.g. have access to built-in reference genomes, etc.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 24 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: james_taylor: Trackster: dense mode features are full height again, don't draw strand indicators when drawing squished features.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix importing library datasets into multiple histories - library datasets will now only be imported into those checked.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for generating metadata in tool shed repositories for a tool that does not use a tool_data_table entry for a dynamic SelectField input parameter.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add locale files for Chinese provided by hanfeisun.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update FASTQ Groomer tool help to indicate that Illumina 1.8+ is Sanger encoded.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Remove "-targetNotSorted" argument from GATK indel realigner: vanished without warning or notice.   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: Fix copy/paste errors in histry contents API   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Repack of .js   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to enter a new tool panel section label when installing repositories with tools from a tool shed in addition to being able to choose an existing tool panel section for containing the tools. Also clean up code related to message displayed when a local Galaxy instance is missing tools required by an imported workflow.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GeneTrack help.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate the non-functional PacBio tools from the distribution and the sample tool config.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix an exception class that doesn't exist. Thanks Oleksandr Moskalenko.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix for slug check flag pointed out by Andrew Warren.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Make toggle icons use black and white and color on hover to match other Trackster icons.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: use icon to set track mode.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix grid operations for use in UserListGrid to allow for Delete, Undelete, Purge of users if the allow_user_deletion config setting is true.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for renaming a tool shed repository - hopefully resolves race condition.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fixes for Data source async controller.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Make history UI icons compatible with changes in 9dbc82483bd2.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Tool help updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add baseline support for handling data types included in tool shed repositories, add the ability to upload files to tool shed repositories by entering a URL in the upload form, provide much better file content checking when uploading either single files or archives to a tool shed repository (niether html content nor images are currently allowed), enhance error messaging when tool config parameter tags are not functionally correct.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Revert file content checks when up0loading to a tool shed repository as they're currently too restrictive.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Bump FastQC version in preparation for updating executable version   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Use mercurial's purge extension to remove untracked repository files and empty directories, and fix a bug related to deleting repository files.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: External display applications will now return HTTP not found for non-existant parameters/datasets when requested.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add 'type_extension' attribute to datatypes_conf.xml that allows creating a datatype from an earlier declared datatype by referencing extension. Make several datatypes that had been direct instantiations from Data become subclasses of Binary.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: A tool shed admin will now receive content alerts (as part of the alert message) for each file uploaded to a repository that contains either image content or html content if the admin has chosen to receive email alerts for changes to the repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Rename toggle-contract to toggle in CSS so that CSS class name matches icon file name.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Fixes for the new horrible FastQC html layout. Now wastes a whole lot of space on the left   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in Trackster's 'Add Datasets to Visualization' button.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: significant refactoring to unify Drawables' HTML structure and also facilitate customization. Groups now use icons and can show/hide content.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add EMBOSS citation to EMBOSS tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add information for UCSC data to annotation profiler.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Improve exception handling when loading and displaying tools in the tool shed, check content of files uploaded to a tool shed repository only when necessary, and clarify that borwsing repository files is only available for the repository tip.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Tophat functional tests for tool version 1.3.3   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Refactor data providers to use the get_iterator/process_data framework whenever providing individual data points.   Bitbucket
• [galaxy-commits] commit/galaxy-central: epaniagu: fix tool_form.mako js typo affecting "drill_down" input   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: When fetching BAM data for Trackster, use BAI from metadata when possible rather than waiting for converted dataset with duplicate BAI.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GATK to version 1.3.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add DepthOfCoverage GATK tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update tool_conf.xml.sample.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack js scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Commit missing template for user impersonation (Thanks Dan).   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster performance improvements: (a) build tile messages only once during tile creation and (b) move tiles rather than show/hide tiles when scrolling.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GenomeSpace import from file browser tool to use new versioned API.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Do not use route memory when creating URLs to metadata files.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add disk_usage methods to tool shed's User model object - fixes server error when viewing User Preferences.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update test data for cufflinks v1.1.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Cuffcompare test data to be compatible with v1.1.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Cuffdiff test data to be compatible with v1.1.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: Bug fixes for the ctd tool   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to reset all metadata (for every change set) in a tool shed repository (currently restricted to an admin), and add a fix for checking security when making changes to tool shed repository information on the Manage repsoitory page.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix GFFDataProvider bugs introduced in 9b7d5c1c0be6.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix Tile variable name so that it connotes what it actually stores.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add picard_FastqToSam.xml and picard_SamToFastq.xml to tool_conf.xml.main.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update modified generic GATK 1.3 arguments.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Subtle but critical fixes in resetting all metadata for tool shed repositories ( and some code clean up ).   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for generating metadata on the repository tip.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Remove --rodToIntervalTrackName from GATK tools; not present in version 1.3.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add SAMTools mpileup.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Remove no longer supported ROD datatypes from GATK tools (version 1.3).   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update help for some SAMTools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Updates for GenomeSpace file browser importer.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance User preferences within a Galaxy tool shed to enable users to elect to receive email when content is first uploaded to a new repository. Also add a new grid interface to enable users to easily manage registering with any tool shed respositories to receive email when changes are made to the selected repositories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have fimo.xml use fields.path approach instead of directly filtering on data table.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for Galaxy / tool shed communication.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: More fixes for Galaxy <-> tool shed communication.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: refactor action icon creation and initialization.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Remove the old template_path setting from community_wsgi.ini. since it is set incorrecly and not neede anyway.   Bitbucket
• [galaxy-commits] commit/galaxy-central: hanfeisun: Modify some string in Mako templetes for complete i18n support.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: Added "Convert CG MasterVar file to pgSnp format" tool to the Human Genome Variation section   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: "Convert CG MasterVar file to pgSnp format" tool and test data   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update Yogeshwar Kelkar's microsatellite tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Support display of extra files/composite types in published items. Fixes #628   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Make the use of the 'require_login' config setting functionally correct for the tool shed, and debug it's use in the Galaxy framework as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance the process for displaying a workflow in a tool shed repository so that workflows in change sets other than the repository tip can be viewed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Updates for 'GenomeSpace import from file browser' tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Updates for GATK tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor fix for 04e8ed0cd930.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: python version of "phyloP interspecies conservation scores" tool   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add no_options validator to built-in reference genome selector in GATK tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for 2ee4a6b8419b where chromInfo from custom dbkeys when no custom dbkeys have been defined would cause an error.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Apply HTML escaping when editing dataset name.   Bitbucket

Last message date: Wed Nov 30 22:51:58 EST 2011
Archived on: Wed Nov 30 22:52:12 EST 2011

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