November 2011 Archives by subject

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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: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 24 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   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: dan: Add DepthOfCoverage GATK tool.   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: dan: Add no_options validator to built-in reference genome selector in GATK tools.   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: Add SAMTools mpileup.   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: dan: External display applications will now return HTTP not found for non-existant parameters/datasets when requested.   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: dan: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for implicit dataset conversion that was broken in 1827729ed37e.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix label for 'How to specify bad variants' in variant_recalibrator.xml   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fixes for Data source async controller.   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: dan: Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor fix for 04e8ed0cd930.   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: dan: Remove --rodToIntervalTrackName from GATK tools; not present in version 1.3.   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: 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: 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: dan: Tool help updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update tool_conf.xml.sample.   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: Update GATK to version 1.3.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GeneTrack help.   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: dan: Update help for some SAMTools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update modified generic GATK 1.3 arguments.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update Yogeshwar Kelkar's microsatellite tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Updates for GenomeSpace file browser importer.   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: dannon: Fix bug introduced in 0ba260ea43c4 for displaying workflows.   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: dannon: Fix for slug check flag pointed out by Andrew Warren.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Repack of .js   Bitbucket
• [galaxy-commits] commit/galaxy-central: epaniagu: fix tool_form.mako js typo affecting "drill_down" input   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Bump FastQC version in preparation for updating executable version   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: 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: 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: 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: Add disk_usage methods to tool shed's User model object - fixes server error when viewing User Preferences.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add locale files for Chinese provided by hanfeisun.   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: 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: greg: Eliminate the non-functional PacBio tools from the distribution and the sample tool config.   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: 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: 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: 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: Fix for generating metadata on the repository tip.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for renaming a tool shed repository - hopefully resolves race condition.   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: 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: Fixes for Galaxy / tool shed communication.   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: 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: More fixes for Galaxy <-> tool shed communication.   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: 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: greg: Revert file content checks when up0loading to a tool shed repository as they're currently too restrictive.   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: Temporary work-arounds for dealing with Galaxy panels when switching from workflow UI and Galaxy UI.   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: 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: hanfeisun: Modify some string in Mako templetes for complete i18n support.   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: jgoecks: Apply HTML escaping when editing dataset name.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Do not use route memory when creating URLs to metadata files.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in Trackster's 'Add Datasets to Visualization' button.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug introduced in f34a17e508e5.   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: jgoecks: Fix vertical scrolling via keyboard in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Improve Cufflinks' documentation for gene annotation dataset parameters.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Make history UI icons compatible with changes in 9dbc82483bd2.   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: Pack js scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.   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: jgoecks: Remove debugging statements from f34a17e508e5.   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: jgoecks: Support display of extra files/composite types in published items. Fixes #628   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: jgoecks: Trackster: (a) give every Drawable unique id and (b) remove unused reference to jquery.scrollTo.   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: Trackster: fix bug in showing 'add datasets' button and rename update_track_icons to update_icons for clarity.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: refactor action icon creation and initialization.   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: jgoecks: Trackster: use icon to set track mode.   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: jgoecks: Update test data for cufflinks v1.1.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Tophat functional tests for tool version 1.3.3   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Use panels when adding a build from a new track browser.   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: John Duddy: Fix copy/paste errors in histry contents API   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: Fix signature of slit method   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: 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: Commit missing template for user impersonation (Thanks Dan).   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix a typo in tasks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix an exception class that doesn't exist. Thanks Oleksandr Moskalenko.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Invalidate other Galaxy sessions upon password change. Thanks Bob Harris!   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: richard_burhans: "Convert CG MasterVar file to pgSnp format" tool and test data   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: Bug fixes for the ctd tool   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: consolidated make_html_table for tabular datatypes   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: python version of "phyloP interspecies conservation scores" tool   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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