July 2011 Archives by thread

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Starting: Sun Jul 3 15:05:34 EDT 2011
Ending: Fri Jul 29 14:33:43 EDT 2011
Messages: 67

• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: provide option to fetch additional data when not all data initially fetched for a tile. For now, all data is refetched rather than iterative fetching. As part of this functionality: (a) enable data providers to accept a max_vals parameter that is used to fetch a particular number of values; and (b) Trackster caches now ignore items with stale=true.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster refactoring: (a) change data_cache attributes to data_manager to reflect attribute type; (b) automatically use track mode and track view's chrom when getting data from the manager; and (c) calculate and store low, high for Tiles to facilitate reuse.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: add infrastructure for getting data iteratively but, for now, still fetch all data when getting more data. Use Galaxy button styles as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: implement start_val parameter for data providers and use parameter to provide incremental fetching of data. Only 'deep' fetching is currently supported.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: More comprehensive error detection for weblogo installation or execution errors   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Add tool version-string support to tool wrappers. Use the <version_string> tag to denote the command to run for the tool version, such as: tophat --version (see tophat wrapper change for example)   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: implement broad/wide incremental data fetching and add icons for data fetching.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update annotation profiler tool sample configuration file.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix a bug when setting default history permissions in the user preferences; receiving method now gets all required params.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: First pass implementation for tool shed repository metadata. This implementation currently provides a baseline metadata collection for tools in a tool shed repository. This change set also includes the implementation for displaying a tool UI for each valid tool config in the tool shed repository. Fixes issue # 565.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Allow an admin user to manage repositories they do not own.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Bug fix for setting tool shed repository metadata on repositories containing more than 1 tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for setting tool shed repository etadata multiple times when nothing in the repository has changed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for displaying tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: peterjc: Support new tool version tag in NCBI BLAST+ wrappers   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Rename version_string -> version_command, update wrappers   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Improve BLAST parser tool error handling, and improve elementtree import as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are:   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add support for exproted Galaxy workflows when generating metadata for a tool shed repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: document FeaturePainter object and methods as abstract.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Change tool shed repository version to be revision, and some fixes for generating and saving repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Another patch from Assaf Gordon for the cleanup_datasets.py script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in trackster filtering of GFF datasets.   Bitbucket
• [galaxy-commits] commit/galaxy-central: guru: Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: show 'Add Datasets' button when there are no tracks in a visualization. Refactor and modularize add tracks code so that is can be used in multiple places.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Case sensitivity note for login not found error.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Various tool shed fixes and enhancements:   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add exception handling around all mercurial api commit calls. On Linux, the mercurial api's commit seems to bump into issues intermittently, throws an exception, and rolls back the transaction. Although I can reproduce it on Linux, I cannot produce this behavior on a Mac. The exception handler uses a different approach to committing the changes. I've also added this code to the update_for_browsing method.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for message display when setting tool shed repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Fix LibraryField grouping issue by adding prefix   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: Minor tweak to the x axis sorting of Manhattan plots to fix the fact that in R, unique() returns an alphabetically sorted list - need to use sort on the result to get correct lexicographic (10 comes after 9 eg) on the X axis...   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Several tool shed enhancements and fixes:   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix filtering of deleted objects in grid framework when using sqlite. Also make history grid's label for deleted filter clearer. Fixes #596   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Fix bitbucket issue #612 regarding administrative job lock toggling inappropriately. Split logical forms into actual forms.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add exception handling for mercurial commands that break in the test / production tool shed environment, but not elsewhere.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Remove tool shed repository files from disk that become untracked because they were removed from the repository within an exception block (only occurs in the tool shed test / production environments ).   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for tool configs that do not include a command tag.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add Assaf Gordon's collect_job_timings.sh script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: save data in Tile object and use to determine if filters are available.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Prevent keyboard navigation from within input elements in shared visualizations.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to view all stored metadata for each tool in a tool shed repository, as well as some tool attributes that are not stored as metadata (e.g., tool.command, etc ).   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: enable datasets without a set dbkey to be added to a visualization.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster documentation.   Bitbucket
• [galaxy-commits] commit/galaxy-central: trevorw: minor whitespace updates, tab/space consistency   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: tool_form should overflow correctly   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Cleaner fix for 5828:e34b1108f7f8   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Move a number of dataset-related methods from the root controller to the dataset controller and encode their ids. Also add user disk usage accounting.   Bitbucket
• [galaxy-commits] commit/galaxy-central: guru: Added additional options to the liftOver tool. It now supports GFF and GTF formats and allows multiple output regions and related options.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Closed the feature/ws branch, changes from this branch were merged in 5827:f3a1086fac91.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 5 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add necessary import statement for e7214c69ed7d.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Rewrite Pac Bio assembly_stats tool - it now takes 1 input fasta dataset and produces 1 output tabular dataset. The "wiki" output format has been eliminated, and the dependency on the pbpy module has been eliiminated.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug in 3d2fd67bc0ca that prevented autocomplete from working in dataset attributes editing page.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix bug discovered by Glen Beane in rendering roles on the permissions page for data libraries. In the data library hierarchy, rendered roles are all derived from roles associated with the LIBRARY_ACCESS permission, but roles rendered for that permission itself must be handled as a special case, which now is the case in that all legitimate roles not associated are listed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Mke message stating how much disk space was cleaned up in the Galaxy reposrts prettier. Fixes issue # 618.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Tool shed template fixes: replace 1/2 template somehow removed in change set 5830, fix pop-up menu code for tools.   Bitbucket

Last message date: Fri Jul 29 14:33:43 EDT 2011
Archived on: Fri Jul 29 14:33:48 EDT 2011

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