January 2012 Archives by subject

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Starting: Tue Jan 3 09:14:21 EST 2012
Ending: Tue Jan 31 15:58:53 EST 2012
Messages: 95

• [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: 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: 4 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 6 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add GATK Print Reads walker tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add GATK VariantSelect tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add mpileup to tool_conf.xml.main.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add Perform Logistic Regression with vif, Compute partial R square, and Assign weighted-average to tool_conf.xml.main.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add sort tag to Print Reads test output element.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Better handling of JEXL expressions in GATK.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Better handling of JexlExpressions in stratification expressions for GATK VariantEval.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Enhance Picard SamToFastq to allow read group aware processing.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for setting up column assignments for dynamic options wrt tool data tables when the index file is missing.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: GATK Updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: GATK: add newly introduced gatkreport datatype, currently used by variant eval.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have GOPs Concatenate tool always respect the provided strand column.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: On edit attributes page, make the info field a textarea. Also HTML escape the contents of data_annotation and info textareas.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GATK to version 1.4.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update samtools flag stat test data.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update tool test for GATK Print Reads.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix for Dan's issues with the GATK tools not behaving properly in 'set at runtime' mode in workflows.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix for Input Dataset datatype filtering regression introduced in 6329:ab90893a7cf5.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add columns for datatypes and workflows in the tool shed repository metadata grid.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add more flexibility in generating a workflow image in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add support for handling datatype display applications in datatypes_conf.xml files included in installed tool shed repositories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to deactivate / activate installed tool shed repositories. When a repository is deactivated, it's contained tools are eliminated from the tool panel on the fly. Similarly, if a deactivated repository is activated, it's contained tools are loaded into the tool panel on the fly. This works for tools contained in sections or outside sections in the tool panel.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the drmaa_external_runjob_script attribute to the tool shed's config so that setting repositroy metadata works.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance the process of deactivating / activating installed tool shed repositories by handling the deactivation / reactivation of proprietary datatypes, datatype converters and display applications.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhance the process used by objects to retrieve tools from the tools_by_id dictionary. This allows for workflows that were built with tools originally included in the Galaxy distribution but later moved to the tool shed to function correctly if the tools are installed from the tool shed using Galaxy's update manager. In addition, workflows that were built using locally developed and hosted tools, but the tools were included in a tool shed repository, removed from the local instance, and then installed from the tool shed to function correctly. This approach works for the rerun button on history items as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for comparing workflows in repository metadata when resetting all metadata on a tool shed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for generating workflow metadata and viewing workflows in tool shed repositories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for getting a tool in the API workflow component.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for loading tools from tool config(s).   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for loading tools - bug introduced in my last commit...   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for reloading a tool in the tool panel - make sure to keep the tool's tool shed related attributes when the tool is reloaded. Also make sure to send the guid attribute when loading a tool into the tool panel if the tool is contained in an installed tool shed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for searching for workflows in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for setting tool shed repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes and enhancements for supporting tool shed repositories that include data types that use class modules included in the repository. More than 1 class modules can now be included in the repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes for Galaxy instance , => tool shed communciation where Galaxy instance is running behind apache with rewrite rules.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: In addition to deactivating / reactivating installed tool shed repositories, add the ability to uninstall / reinstall installed tool shed repositories. Uninstalling and reinstalling will affect the repository on disk as well as the tool config files in which the tool shed repostory's tools are defined. Reinstalling a tool shed repository will currently load it's tools into the same location in the tool panel in which the tools were originally located prior to uninstalling the repository. Installing / uninstalling / deactivating / activating work for tools sheds that were installed either manually be a Galaxy admin or automatically installed by the Galaxy installation manager for those repositories that contain tools tha tused to be in the Galaxy distribution but have since been moved to the main Galaxy tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Replace None with an empty string when creating tool panel Elements for installed repository tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: When storing tool panel section information for installed repository tools, make sure tool section id, name and version values are an empty string rather than None.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store.   Bitbucket
• [galaxy-commits] commit/galaxy-central: guru: added cacao genome to manual builds   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add href to trackster icons in history pane so that browser treats it as a URL and not an anchor.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Do not find valid chroms because this is computationally expensive and not currently used.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in saving visualizations.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix jQuery 1.7 compatibility bug so that multi-selects are not replaced by search+select and pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Handle NaN values to produce correct JSON in data providers.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Improve language in 'Import workflow' dialog.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack trackster script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove spurious export in run functional tests scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Standardize code and error messages on 'public name' rather than 'username'   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Subset GFF datasets correctly when running tools in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: bug fix when padding tiles for display.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: clear track content during initialization.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: enable composite tracks composed of a FeatureTrack and LineTrack. Refactor to always handle left_offset only in draw_helper.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix reference track display bug.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bug with multiple color pickers in track config.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bugs in summary tree display & pack script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bugs to (a) clear reference track when changing chromosomes and (b) to only show differences if reference data is available.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix drawing bug when clear_after is true.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: gentler compositing and refactoring so that compositing operations are at appropriate level.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: inline editing of LineTrack min and max values.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: more object-specific equality operators.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: refactoring in preparation for multi-track filtering.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: true replacement of a track with a group when running a tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update functional tests to be compatible with 0d1d62b8be2e   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Tophat tests for v1.4.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Usability improvements: (a) standardize and simplify language for using visualizations; (b) new icon for adding datasets to trackster; and (c) simpler UI for adding dataset to new/saved visualization.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: User check when fetching visualization chrom information.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jmchilton: Specify Java temp directory for picard execution should match   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: Add support for generic XML files for tool integrations   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Add tool_dependency_dir to the sample config.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Add missing distributed object store config file option to the sample universe_wsgi.ini.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Avoid annoying errors produced by the Googlebot hitting the import library datasets to history page (it doesn't have a history).   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Bugfix for distributed object store that prevented certain kwargs from being passed to certain methods in the backend store.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Ensure that the history export dataset is created when the job is created.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Filesystem free space checking for the object store.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix for the object store doctest.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix unit tests on Python 2.5 (can't load s3_multipart_upload.py).   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Ignore DrmCommunicationException when checking job state. Thanks Ed Kirton.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: In the local job runner, use NamedTemporaryFiles rather than subprocess.PIPEs to prevent Popen from hanging when a lot of data is written to STDOUT/STDERR. Fixes #662.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make paths to metadata temp files absolute.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Object store fixes for Python 2.5. S3 not currently supported on 2.5, although it can most likely be worked around.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Object Store: Store the backend object store's ID in the database when using the distributed object store.   Bitbucket

Last message date: Tue Jan 31 15:58:53 EST 2012
Archived on: Tue Jan 31 15:59:05 EST 2012

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