April 2012 Archives by thread

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Starting: Mon Apr 2 10:09:06 EDT 2012
Ending: Mon Apr 30 16:28:03 EDT 2012
Messages: 170

• [galaxy-commits] commit/galaxy-central: dan: Fix for --multiallelic in Unified Genotyper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for call to object_store.update_from_file for collect primary data in tools/__init__.py.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for DiskObjectStore._construct_path recieving extra keywords.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: If installing a single tool shed repository that contains a readme file, display its contents on the tool panel section selection page.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 11 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Make sure repository files displayed during installation are restricted to a max file size and contents are viewable in a browser.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Update cloud launch config name.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: changes to aaChanges interface   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: I missed a call to a renamed method in the job manager.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add a counter utility to the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Make sure a valid tool has a guid.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix variable name bug that occurred when rendering tool links outside a section.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix inflector for n == 0   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: In the DistributedObjectStore, when update_from_file is called with create=True, call DistributedObjectStore.create().   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Include invalid tools in repository metadata, and enable the admin to reset all repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Handle exceptions when resetting all repository metadata in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Warn users against navigating away from Galaxy while uploads are in progress, to prevent interrupting uploads.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enable an admin to be able to view and regenerate tool shed statistics.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for shed statistics.   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: fubar: Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Allow multiple output file collection from the job_working_directory.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix multi-input workflow selector to account for recent structural changes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug that scrolled Trackster on double click when completely zoomed in.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Rework the display of DrillDown form elements.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to browse invalid tools in the tool shed - current user is restricted to seeing only their invalid tools if not an admin. Also a bit of cleanup in tool shed statistics.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Apply fix for brand overflowing to the tool shed's base_panels.mako.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Slight fix for viewing invalid tools - allow an admin user to view only his invalid tools if requesting from the repositories view.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Only include invalid tools in the metadata for the repository tip - supporting this in older revisions is a bit more complex and will be supported at a later time.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: DrillDown parameter now uses slideUp/Down.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: All models have id attribute, so do not declare explicitly.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Create ui.js for generic UI Backbone functionality and add models & views to display icon menus. Use new functionality for visualization menu.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add some missing cgi.escape calls around values in form_builder.py.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add some missing cgi.escape calls around values in form_builder.py.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: In tool_form, have call to unicode on non unicode field_html use 'replace' instead of raising a server error. Fixes issues seen with non unicode characters in history item names.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix missing import in job manager.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Track and reuse HDA subsets in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bugs in data fetching for tracks created via tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug that prevented actions from being taken on left panel.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Miller Lab's Genome Diversity tools moved to the Tool Shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Simplify and generalize tool menu container style.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for not showing hidden tools in tool panel.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fold tool panel styles back into base.css and include new style for tool panel in panel (w/o iframe).   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: fix path to proprietary_datatype_module so that we get the correct error message when an import fails   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Comment out recently used tool update for now because it is not implemented yet.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: remove Genome Diversity {test, tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Do not add hidden tools to the tool panel.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for BWA -R option.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Small fixes for Trackster icons   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: add column names   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add argument names to parameter help for GATK Advanced options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update argument names to parameter help for GATK Advanced options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix history_contents API adding the HDA to the history twice (resulting in skipped hids)   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Whitespace cleanup.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix inconsequential warning about when tag when loading samtools mpileup.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix inconsequential warning about when tag when loading FreeBayes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add argument names to parameter help for GATK tools' options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: New config option, and change in default behavior regarding dataset path display in View Details. Administrators can now *always* see the full path, and if the expose_dataset_path option is True, so can regular users.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Create object to store Galaxy paths for use in JavaScript.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Cloud Launch - Password Field for AWS Secret instead of plain text input   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Basic functionality for accessing the API through session (if available) instead of via API key. Needs refactoring to combine _ensure_valid_session and transaction types.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Move tools controller from UI controller to an API controller and add show method for tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Incremental display for tabular datatypes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Tabular dataset display - Remove logs, revert scroll detection to base.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove enable_api flag; API is now enabled by default and cannot be disabled.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Rework OpenID process.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor fix for clicking an OpenID provider to refresh credentials.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix two more places where filenames in content-dispositions were not being surrounded by quotes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Use javascript:void(0) rather than # in tool section links to avoid unwanted scrolling to top of page.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor tweeks for redirect flow during OpenID process.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 7 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Tweek for empty referer value causing OpenID verification failure.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow GenomeSpace OpenID provider for log in.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Quick fix for screencasts. TODO: Modal/overlay javascript needs to use the height/width parameters.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for workflow module.__get_tool_version.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix for cleanup_datasets.py when database_connection is the uncommented default in the config file.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Use hash as location in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix for displaying tools outside of a section.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate duplicate galaxy.datatypes.images:Xpm sniffer entry from datatypes_conf.xml.sample.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Moved Genome Diversity tools to toolshed, removed from main tool_conf.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Handle exceptions caused by invalid tool configs when setting repository metadata in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Attempt to correctly render dynamically generated select lists when previewing a tool in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Allow for starting/stopping multiple servers directly in run.sh.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Significantly improve handling of SAM rendering with the new tabular display. Optional parameters are accounted for now.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Do not use template for tool panel label as it is overkill.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow BCF files to be uploaded.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for handling proprietary datatypes included in a tool shed repository being installed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add skeleton for datasets API controller.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Tool shed repository metadata fixes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make the new tabular column_names metadata element optional.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: (a) fix bug in setting up browser router and (b) use events to notify router that view navigation has occurred.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for setting tool versions and fix for setting repository metadata for tools in an installed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Workflow outputs logic rewrite. Accounts for old workflows that have no outputs defined but do use HideDatasetActions.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Branch close.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Tophat wrapper: (a) add documentation for versions supported and (b) always return insertions and deletetions outputs.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Use secure gravatar server for images.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: use strand coloring for FeatureTracks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for setting tool shed repository metadata, and enhance the hg command line handler to reset all metadata on a repository to which a push is occurring.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for LibraryDatasetDatasetAssociation.templates_dict when a content value is not set.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Handle errors in the job handler caused by idata.hid being None.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix decode issues with library datasets in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove spurious comments from templates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add a running_functional_tests config setting.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix missing sanitize_html import.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Enable interval datasets to be visualized in trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Updates to tabular chunked display to force text content of cells. (fixes VCF display)   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix zipfile failure for composite datatypes. Rename variables in data.display method to be consistent with 'data' for hda naming convention. Remove duplicated comment from tabular_chunked.mako.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Slightly more unique automatically generated filename for GenomeSpace export.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add a transform_publicname method that coerces a provided string into a valid username. This is now used during user creation.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Tweak for 7079:7ca527380818.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: correctly handle navigation when only chrom name is used and name is the same as chrom currently being viewed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for clearing implicitly converted dataset association when converted dataset is deleted.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: do not subset data with no detail.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: better handling of resizing and navigation. Pack script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix heavy handed removal of PJAs when not using outputs.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Use the mercurial api for all tool shed hg actions.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Basic support for Tophat2.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Merge   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for setting repository metadata on older change sets in a tool shed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: More fixes for setting tool shed repsoitory metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Refactor and simply tophat wrapper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Partial revert for c32b71dcfc84.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Better message when creating a custom build.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Provide mercurial as an egg for tool shed operations.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix the tasks runner that I broke when I split job management into multiple processes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for getting updates to an installed tool shed repository where no updates are available.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: More fixes for retrieving updates for an installed tool shed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Trinity wrapper to support most recent versions.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance the "find workflows" feature in the tool shed and installe dtool shed repositories to allow for finding all workflows if the search criteria is blank.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add fusion search parameters to Tophat wrapper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Minor curation of data providers: (a) rename gff data provider to match similar providers and (b) add note about how to extend GTF tabix to support GFF/GFF3 as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Workflow editor fix for the case where RenameActions had null action arguments vs being unspecified or {} as expected. This situation exists in very few rename actions and hasn't been reproduced, may be legacy workflow steps.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add rerun and show info buttons to discarded datasets.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for installing from a list of tool shed repositories that matched a search criteria.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Include more Tophat2 options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix class assignment for links/menus/popups in grids.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add basic tool execution to the API.   Bitbucket
• [galaxy-commits] commit/galaxy-central: anton: Modified metagenomic mapper to use BLAST+ blastn in megablast mode   Bitbucket
• [galaxy-commits] commit/galaxy-central: anton: Fixed number of threads   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Make history export work for optional data inputs.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix version references in tophat2 wrapper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove version code from tophat wrappers as this is now handled by <version> tag.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Skeleton wrapper for Bowtie2.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: More cleaning of Tophat wrapper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have implicit SAM to BAM converter sort the output BAM file so that indexing will not fail.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for some requests sent from Galaxy to a tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Revert Tophat wrapper due to parameter incompatibility issues.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Revert Tophat wrapper version #.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Extract workflow - fix nested dataset input mapping.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate resetting all repository metadata on a tool shed repostiory when its not necessary.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Allow for library deletion from the API (admins only).   Bitbucket

Last message date: Mon Apr 30 16:28:03 EDT 2012
Archived on: Mon Apr 30 16:28:06 EDT 2012

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