January 2012 Archives by date

• Messages sorted by: [ thread ] [ subject ] [ author ]
• More info on this list...

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: 6 new changesets   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: Trackster: clear track content during initialization.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Handle NaN values to produce correct JSON in data providers.   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: 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: 2 new changesets   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: jgoecks: Trackster: fix bug with multiple color pickers in track config.   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
• [galaxy-commits] commit/galaxy-central: 3 new changesets   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: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make paths to metadata temp files absolute.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: User check when fetching visualization chrom information.   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: Fix bug in saving visualizations.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Better handling of JexlExpressions in stratification expressions for GATK VariantEval.   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: jgoecks: Standardize code and error messages on 'public name' rather than 'username'   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack trackster script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: bug fix when padding tiles for display.   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: natefoo: Add missing distributed object store config file option to the sample universe_wsgi.ini.   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: jgoecks: Trackster: fix reference track display bug.   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: Fixes for Galaxy instance , => tool shed communciation where Galaxy instance is running behind apache with rewrite rules.   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: 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: natefoo: Filesystem free space checking for the object store.   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: jgoecks: Trackster: true replacement of a track with a group when running a tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Subset GFF datasets correctly when running tools in Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update functional tests to be compatible with 0d1d62b8be2e   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove spurious export in run functional tests scripts.   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 loading tools - bug introduced in my last commit...   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Better handling of JEXL expressions in GATK.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for getting a tool in the API workflow component.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Update Tophat tests for v1.4.0   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Have GOPs Concatenate tool always respect the provided strand column.   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: 24 new changesets   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 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: Add columns for datatypes and workflows in the tool shed repository metadata grid.   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: Fix for comparing workflows in repository metadata when resetting all metadata on a tool shed repository.   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: 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: 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: natefoo: Fix for the object store doctest.   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: 4 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix bugs in summary tree display & pack script.   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: greg: Fix for loading tools from tool config(s).   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Ignore DrmCommunicationException when checking job state. Thanks Ed Kirton.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: GATK Updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Add tool_dependency_dir to the sample config.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: Add support for generic XML files for tool integrations   Bitbucket
• [galaxy-commits] commit/galaxy-central: jmchilton: Specify Java temp directory for picard execution should match   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   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: dan: Update GATK to version 1.4.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: fix drawing bug when clear_after is true.   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: jgoecks: Trackster: refactoring in preparation for multi-track filtering.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Enhance Picard SamToFastq to allow read group aware processing.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add GATK Print Reads walker tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add sort tag to Print Reads test output element.   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: dan: Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix for Input Dataset datatype filtering regression introduced in 6329:ab90893a7cf5.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Improve language in 'Import workflow' dialog.   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: 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: 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: dan: GATK: add newly introduced gatkreport datatype, currently used by variant eval.   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: Ensure that the history export dataset is created when the job is created.   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: guru: added cacao genome to manual builds   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: jgoecks: Trackster: more object-specific equality operators.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: inline editing of LineTrack min and max values.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack scripts.   Bitbucket

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

• Messages sorted by: [ thread ] [ subject ] [ author ]
• More info on this list...