October 2011 Archives by subject

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Starting: Mon Oct 3 10:40:42 EDT 2011
Ending: Mon Oct 31 17:13:38 EDT 2011
Messages: 109

• [galaxy-commits] commit/galaxy-central: 11 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: 2 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: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: "Merge BAM Files" under SAM Tools section(???) calls Picard MergeSamFiles.jar. Update to new jar location.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add a link to allow the user to switch to the new history directly after cloning.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add dataset_metadata_in_data_table validator. Mimics behavior of dataset_metadata_in_file, but uses data tables.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add get info/parameter button to empty datasets in history item view.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add metadata validator to force input bam files to have bam_index metadata files for GATK tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add Picard tools FASTQ to SAM (makes BAM) tool. Add Picard tools SAM to FASTQ tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add Secure Hash/Message Digest tool to tool_conf.xml.main.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add test/development GenomeSpace file importer datasource tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow picard_SamToFastq to use input BAM files.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow Picard based Merge BAM Files tool to work on sam inputs as well as the previously accepted bam.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow specifying a help attribute for repeat parameter grouping.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow toolbox tests to test 0 instances of a repeat.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Clean up for some GATK tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: First pass at updating GATK tools to version 1.2. Changes are not backwards compatible with workflows. Still considered BETA, and so future changes are like to also not be backwards compatible.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for .wiki_url in tool_form.mako   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for 538c42806e79.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for refresh on change in workflow run interface triggering actual running of workflow.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix Tabs to 4 spaces in lib/galaxy/datatypes/genetics.py.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: GATK tools will now use gatk_picard_indexes data table.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: GATK updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have Picard MergeSamFiles use return code to determine tool error.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: HTML escape job stderr/stdout/info on dataset error page.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor cleanup in picard_SamToFastq.xml   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Remove some debug prints from GATK unified genotyper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Show dataset size of non-purged error state history items.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Some genomespace_file_browser tweaks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Some gatk_wrapper.py tweaks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Tweak validator for input bed file in SICER tool to work around workflow editor issue.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update for Sam to Fastq.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GATK command line options for gatk/indel_realigner.xml   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update generic GATK command line options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update Picard tools to use tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update sff extractor to version 0.2.10.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update SRMA wrapper to use data tables.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Workflows: Fix for 5cfec3f4f17c to accommodate workflows with 'input dataset' steps.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Increase size limit for display of html files to 10000000 bytes - mirdeep2 creates very large html objects.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add basic UI for managng tool shed repositories installed into a local Galaxy instance from a tool shed. Add the ability to view the list of tools and workflows included in installed tool shed repositories. Ad the ability to import a workflow from an installed tool shed repository into the local Galaxy instance.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add new tool attributes to hold information about tools installed from a Galaxy tool shed. Enhance the toolbox's <tool> tag parser to handle these new tool attributes for installed tools. Enhance the Workflow import and load functions to search these new attributes when looking for required tools in the Galaxy instance.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to search for tools within tool shed repositories by any combination of tool id, name and version (exact or partial matches).   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to search for workflows by name in a Galalxy tool shed, either within the tool shed itself or in a local Galaxy instance configured to communicate with the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to upload exported Galaxy workflow files. Makew a first pass at fixing bugs when importing a workflow into a Galaxy instance that does not have all of the required tools. This code is still full of bugs.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to view workflows contained in a tool shed repository as svg images. Add the ability to import a specific workflow from a Galaxy tool shed repository to a loacl Galaxy instance. Fix bugs when displaying or running a workflow that requires tools that use the old Galaxy tool id, but the local Galaxy instance uses tools installed from a tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Clarify tool searches in the tool shed. Searches are retricted to only tools that properly load in Galaxy.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Create a new ToolShedRepository record only if necessary - if one already exists for the installed repository but is marked deleted, mark the exisint record undeleted.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Don't display the "User Info" select field when registering as a new user of editing your information as an existing user unless there are existing form definitions that provide options for selection.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate forgotten (and not wanted) PostJobAction code when generating a workflow it's dict representation for rendering as an svg image in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Encode the tool shed repository information and include in the request when installing into local Galaxy instances rather than using cookies.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance automatic tool shed repository installation to enable installation of multiple repositories using a multi-select frid layout instead of installing just a single repository at a time.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance tool searching in tool shed repositories to enable multiple values in any of tool_id, tool_name, tool_version. In the tool shed search form, taking advantage of this feature requires comma-separated lists to be entered in the form fields.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhanced Galaxy instance <=> Galaxy tool shed integration:   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for loading a workflow that contains tools whose tools ids are the old version of tools ids, but whose available tools use the new tool guids as the tool id because the tools were installed from a Galaxy tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for rendering workflow metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes and code cleanup for searching for tools in tool shed repositories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for finding tools installed from a tool shed when building workflows from the current history or running workflows, and the workflow in question references tools using the old tool_id.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for searching for and installing tools from a tool shed. The value of the webapp request parameter is heavily used throughout this process, and has been added to all grid forms that include operation buttons.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Keep track ot the changeset revision when viewing tool shed repositories retrieved from tool searches.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Make sure the same key is used in encoding and decoding between Galaxy and the tool sheds.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Miscellaneous enhancements for the tool shed:   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: More menu options when viewing repostiroy tools in a tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Sort the list of tool shed repositories by name when populating the grid for matching tools, but eliminate all grid column sorting.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jen: Other genome description: corrected typo.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jen: Other genome description: revised all, corrected canonical male   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Better handling of reference data in Trackster read tracks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Bug fixes to Trackster ReferenceDataManager.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Bug fixes: (a) trackster: don't cache tile if undefined and (b) define init_operation_buttons differently to prevent ordering issue. Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Enhance Trackster VCF support: (a) use ReadPainter rather than VariantPainter and (b) provide support for insertions and deletions. Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in saving trackster bookmarks.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in setting shared visualization's viewport.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix for getting reference data for a built-in genome build.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix Trackster bug that prevented differences from being displayed in mapped reads.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix typos.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Force absolute path when creating temporary directory used when importing histories. Fixes #667   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Grid UI fixes: (a) make operation buttons work after refresh and (b) show message each time.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Handle scores with value '.' in data providers.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Improvements to Trackster filters: (a) scaler framework replaces generator framework; (b) addition of height scaler to set feature height based on attributes; and (c) no transparency for feature labels.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Make implicit dataset conversion work with changes in 1827729ed37e.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove duplicate history links in copy datasets done message.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Set URL for visualization when it is first saved.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: add feature-position mapper so that a feature's data can be recovered using from screen position. This is the foundation for providing feature data on mouseover and/or click.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: automatically remove spaces from an entered location.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix display of reference data.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bug in drawing reference track.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: in pack mode for feature tracks, show feature details on mouseover. Also: (a) provide general method for rounding numbers; (b) return numerical filter values as floats rather than strings; and (c) pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: make overview its own track, add icons for showing/hiding overview, and make track header optional.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: no need to parse floats because data providers now return floats rather than strings.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: refactoring to remove (a) references to view.tracks because view can hold any drawable option and (b) track ids because they are no longer used.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: replace menus with icons + tooltips. Overview is not yet implemented.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: return drawing coordinates for all features. Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: set new track color randomly using W3C metrics.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: When copying datasets, provide links to target histories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Force octet-stream MIME only when downloading datasets to prevent Safari from appending MIME extension   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Grouping tool: make error clearer when a line doesn't have entry on grouped column   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Standardize {datatypes|tool}_conf.xml.sample with 2 space indentation and newline before <label> blocks   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: A much more efficient query for calculating a history's disk usage.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix for Python 2.4.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make purged histories visible in the history list grid, make any history viewable from the grid.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: PBS cluster error user messages now suggest retrying the job.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Remove incorrect #-S /bin/bash (SGE shell override) from drmaa job runner. If you were depending on this to get jobs to run on your SGE cluster under bash, please add '-S /bin/bash' to your Galaxy user's ~/.sge_request.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: UI enhancements for purging histories and deleted datasets in a history.   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: I had an older tabular.py, fixed one line that got changed by mistake   Bitbucket
• [galaxy-commits] commit/galaxy-central: richard_burhans: refactored Tabular.make_html_table()   Bitbucket

Last message date: Mon Oct 31 17:13:38 EDT 2011
Archived on: Mon Oct 31 17:13:40 EDT 2011

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