August 2011 Archives by author

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Starting: Mon Aug 1 17:35:26 EDT 2011
Ending: Wed Aug 31 16:51:04 EDT 2011
Messages: 106

• [galaxy-commits] commit/galaxy-central: kanwei: LibraryDataset Parameter:   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update EuPathDB datasource configuration file. Contributed by Mark Heiges.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for 2 comments in templates/dataset/security_common.mako.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: refactor post-draw actions into their own methods.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add a malicious flag to the tool shed's repository metadata - if true, downloading is restricted to only those users that can write to the repository. Fix a bug in determining if a user can write to a repository, and a bit of miscellaneous cleanup.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: A couple of fixes in the manage_repository.mako template.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update GMAJ: fixes a ClassCastException that was encountered on Macs running Java 1.6.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: workflows: Fix for rename not updating latest_workflow in addition to the stored workflow. This fixes the error where workflow exports always had the *original* workflow name, regardless of renames.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Workflows: Same fix as previous, but for rename_async...   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Bugfix for the offline egg packaging script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove unspecified build validators from Cuffdiff wrapper; fixes #631   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Add simple display option to data libraries that omits certain columns... unclutters LibraryDataset parameter UI   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: User/group disk quotas.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Bugfix for check_galaxy (monitor script) since dataset deletion moved to the dataset controller.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Make setting read groups in BWA off by default.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Change Help -> Email comments link to be Support and point to wiki instead of email per Jen's instructions.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Missed a link in previous commit.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: A couple of tool shed template fixes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: get overview working again and pack script.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster overview enhancements: (a) show and hide overview via track menus; (b) use tile cache to store overview tracks; (c) overview track saved and restored.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Update Param unit test to account for the '#' to '__pd__' change from 5810:b68bbdc8dd14 that made it fail.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: only show a dynamic filter if min != max.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fixes, code cleanup for setting tool shed repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Fix for setting repository metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Add missing database migration for quotas (thanks Ross).   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Import patch contributed by Assaf Gordon allowing bwa_wrapper to work directly on fastqillumina formatted files. Closes #635.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for exporting tagged MAF blocks from GMAJ into a Galaxy history.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Fix for unit tests for converting of #/pound   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Refactor validation of user account data--email, username, password--into own module and use module for validating user data throughout Galaxy.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: more fixes for overview functionality.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Fix bug introduced in 1291bc31fec6.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster bug fixes: (a) provide additional vars for drawing histograms; and (b) ensure that FeatureTrack tiles cover track-tile background even when no data is present.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster overview bug fix: always draw for display in visualization and then copy canvas for overview.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Set Trackster overview height correctly.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Very basic "high water mark" per-user job limits.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Documentation and white space fixes for Trackster.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 2 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: peterjc: Add missing requirement and fix incorrect help text in extract sequence tool   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: (1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Change the bugs_email config setting to be the url to our new support wiki.   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability for a tool shed admin to browse repository metadata, and implement fixes for setting repository metadata for repositories with multiple tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Reports: Add a per-user disk usage report.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make nice_size able to display terabytes, and set a default cutoff for users in the user disk usage reports.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dannon: Histories API (jdlogicman) and cleanup.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: A missing flush caused the test for whether a dataset could be removed from disk on user purge to always return False.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Added missing wiki link referred to for eample config settings per Dave & Jen.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability for tool shed users to select repository revisions whose tools can all be successfully loaded into a Galaxy instance in order to view / preview / download various tool versions from a specified repository.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Make the bytes column in the quota table a bigint   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Backed out changeset 6ca0a743296b, Alchemy 0.5 has no BigInteger...   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Monkeypatch BigInt(eger) into SQLAlchemy 0.5 and make the bytes column in the quota table a bigint.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Decrease disk usage and actually remove datasets (if applicable) when purging a history.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Don't count library datasets against the creating user upon dataset creation.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Enhancements and fixes for working with versions of repository tools in the tool shed.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Quota display nice_size bugfixes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/).   Bitbucket
• [galaxy-commits] commit/galaxy-central: 3 new changesets   Bitbucket
• [galaxy-commits] commit/galaxy-central: fubar: WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Spacing fix   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix FTP upload when uploading only a single file and its name contains a comma. util.listify assumes that a string with commas should be split into a list, so don't use listify for this value. Thanks Ilya Chorny.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add FIMO tool from MEME suite.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add FIMO to tool_conf.xml.sample.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Allow FASTQ Groomer tool to work on Color Space files that contain a fake/dummy quality score for the adapter base (e.g. files obtained from the SRA). The Groomer will remove the dummy/fake quality score from the read.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add the ability to switch between tool shed repository revsions when viewing tool metadata.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: make it possible to set features' transparency based on attribute values.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: remove throttling during dynamic filtering because it's not needed with requestAnimationFrame.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Tool versioning: now store version information in hda/ldda tables. Information is kept when copied between hda/ldda, and now displayed in the "Show Info" pages for hdas and lddas.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Simplified Custom Builds page... show less by default   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: route track drawing through requestAnimationFrame framework.   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Fix sam2interval.py bug due to tab spacing   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: Grouping tool: use system numpy if provided, otherwise use bundled numpy egg   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix sending mail when the receipient is a list (as in sample tracking mail routines).   Bitbucket
• [galaxy-commits] commit/galaxy-central: kanwei: sam2interval: Add read_name column   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Cleanup display of shared visualizations.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Minor tool help updates.   Bitbucket
• [galaxy-commits] commit/galaxy-central: John Duddy: APIs to add histories, add items to histories, and list the status   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: create a set of shared functions for managing the user interface and use functions in both visualization editor and display.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: treat numbers as floats when dynamically filtering. Pack scripts.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix SOAPdenovo binary name   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add SICER peak caller.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Fix uploading sorted BAMs to libraries when using the link method rather than copying.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Eliminate the code for the long-unused tool shed datatypes.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: introduce collections of tracks. Track 'groups' can be created and tracks can be added or removed from groups. Currently groups do not have a dropdown menu and cannot be saved.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: add left_offset attribute to LineTrack so that line tracks can be set in overview.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: It turns out that our old version of SQLAlchemy already has the Postgres/MySQL BIGINT types, it just needed the BigInteger SQLAlchemy type and SQLite BIGINT. And fix a bug found by Jack Zhu.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Properly handle error conditions in library_common.upload_dataset when uploading via the API.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add wavelet variance tool contributed by Erika Kvikstad.   Bitbucket
• [galaxy-commits] commit/galaxy-central: greg: Add a guid to tool shed repository tool metadata and add some fixes for previewing tool shed repository tools.   Bitbucket
• [galaxy-commits] commit/galaxy-central: natefoo: Missing import in library_contents.py   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update for wavelet variance tool contributed by Erika Kvikstad.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add SICER to tool_conf.xml.main.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Update FIMO test datasets.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add basic VCF4.1 support.   Bitbucket
• [galaxy-commits] commit/galaxy-central: jgoecks: Trackster: add mode parameter to draw_tile and use to support better overview drawing.   Bitbucket
• [galaxy-commits] commit/galaxy-central: dan: Add samtools rmdup tool.   Bitbucket

Last message date: Wed Aug 31 16:51:04 EDT 2011
Archived on: Wed Aug 31 16:51:07 EDT 2011

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