October 2009 Archives by subject

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Starting: Thu Oct 1 16:26:00 EDT 2009
Ending: Fri Oct 30 17:32:01 EDT 2009
Messages: 206

• [galaxy-dev] /tmp directory   Nate Coraor
• [galaxy-dev] /tmp directory   juan perin
• [galaxy-dev] /tmp directory   Nate Coraor
• [galaxy-dev] [galaxy-bugs] /tmp directory   juan perin
• [galaxy-dev] [galaxy-user] starting workflows with a pool of input files   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2778: Added Cite to masthead   Nate Coraor
• [galaxy-dev] [hg] galaxy 2779: Moving cite to help   Nate Coraor
• [galaxy-dev] [hg] galaxy 2780: Real Job(tm) support for the library upload to...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2781: Adding an option to Group tool to ignore case ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2782: Fixed an error in the help section of the Sam ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2783: Grid states (filter, sorting) can be preserved.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2784: Merge   Nate Coraor
• [galaxy-dev] [hg] galaxy 2785: Fix migration script naming collision.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2786: trackster now supports BED files   Nate Coraor
• [galaxy-dev] [hg] galaxy 2787: Ensure that all user preferences are in unicode.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2788: Turn off grid state preservation.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2789: typo fixes for tools in folders A-M   Nate Coraor
• [galaxy-dev] [hg] galaxy 2790: Paging for grids.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2791: fix history grids   Nate Coraor
• [galaxy-dev] [hg] galaxy 2792: Sample Form definitions:   Nate Coraor
• [galaxy-dev] [hg] galaxy 2793: Association proxy for user preferences.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2794: Asynchronous library upload.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2795: Allow XML includes. Fixes #131   Nate Coraor
• [galaxy-dev] [hg] galaxy 2796: Reintroduce nginx upload module support.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2797: Added grid to view/filter datasets. To view da...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2798: Fix limiting species in interval2maf tool.   Nate Coraor
• [galaxy-dev] [hg] galaxy 2799: Trackster: only attempt dataset conversion onc...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2800: merge   Nate Coraor
• [galaxy-dev] [hg] galaxy 2801: Refactored the library_dataset_dataset_associa...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2802: Functional test fixes for uploading and sniffi...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2803: Prevent script tags in uploads as reported by ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2804: More functional tests for Requests   Nate Coraor
• [galaxy-dev] [hg] galaxy 2805: Requests functional tests: fixed a hack in use...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2806: Fix reporting number of regions processed in M...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2807: Added text trimmer that can be used to groom f...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2808: If you populate a history before logging in, t...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2809: Allow for a specified target for display links...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2810: Fixed trimmer test   Nate Coraor
• [galaxy-dev] [hg] galaxy 2811: Fix spelling of Successfully when running a wo...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2812: Add a new option, 'allow_library_path_paste' t...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2813: Updated BWA and Bowtie wrapper tools so that t...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2814: trackster: feature tracks auto-resize to fit d...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2815: Only allow 'uload files' option when replacing...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2816: A couple bug fixes, additional functional test...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2817: Fix forms and request functional test - broke ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2818: Memory debugging patch from James   Nate Coraor
• [galaxy-dev] [hg] galaxy 2819: Corrected Samtools Pileup tool to accept only ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2820: Eliminate the changed_dependency code introduc...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2821: Corrected problem with assignment of dbkey to ...   Nate Coraor
• [galaxy-dev] [hg] galaxy 2822: fix for trimmer interface   Nate Coraor
• [galaxy-dev] [hg] galaxy 2823: merge   Nate Coraor
• [galaxy-dev] [hg] galaxy 2824: merge   Nate Coraor
• [galaxy-dev] [hg] galaxy 2825: Correct fix for cloning a history - resolves p...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2826: Several small changes to Samtools pileup tool ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2827: Improved paging UI for history grid and added ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2828: Bug fixed in \"compare two queries\" tool. Spe...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2829: Added method get_display_name() to History and...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2830: merge   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2831: bug fix for pilup_parser reported by user   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2832: small tweaks to bowtie & bwa interfaces   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2833: Bug fix for adding a new folder template ( fix...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2834: Allow root/my_data to take but ignore multiple...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2835: Fixing broken tool configs   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2836: Added FASTQ \"Groomer\" tool to converters sec...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2837: refactor trackster, better failure message   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2838: Add Arabidopsis integration at TAIR and UCLA p...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2839: ngs updates   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2840: Reorganization and rewording of history Option...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2841: Added fastq (generic) datatype and deleted fas...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2842: Fixed bug in bed_to_interval_index converter.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2843: Updated several sample index loc files to make...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2844: Incorporate code to provide UCSC and Gbrowse i...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2845: added space to paste tool, removed old solexa ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2846: tiny change to bwa warpper   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2847: Added 'Median' operation to grouping tool   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2848: Removed sniff method from fastqsanger datatype   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2849: Refactored the form validation code   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2850: Fixed ascending/descending bug on Sort, and ad...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2851: More interface updates   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2852: Enables viewing of an importable/sharable hist...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2853: Merge   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2854: Back out history style changes for now.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2855: Add missing tag to template for browing library.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2856: Modified test data and tool conf for fastq stats   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2857: Modified datatypes_conf so fastqsanger type di...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2858: fixed trackster memory leak   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2859: Modified Bowtie wrapper to directly output SAM...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2860: peeking large datasets only displays a portion...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2861: Fixed bug that prevented copying datasets to a...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2862: Increase number of datasets/page on HDA grid.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2863: Proper title for pages   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2864: Encode HDA ids when peeking and saving. Fixes ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2865: Backed out changeset 037374950cc9   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2866: Trimmer fix for fastq processing   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2867: rexpression datatypes and fixes for rgenetics ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2868: added 2 valid chars ; | and patch for empty url...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2869: adding rgenetics converters   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2870: symlinks are not very useful   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2871: Removing another not very useful symlink   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2872: real replacement for stoopid symlink   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2873: Changed FASTQ Groomer's handling of Sanger dat...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2874: Corrected Bowtie wrapper's output type (to SAM...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2875: Changed Bowtie so that if alignment parameters...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2876: trackster: caching works, faster loops, displa...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2877: use files_path not extra_files_path for all ou...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2878: Revert the additional valid_chars added in cha...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2879: Add new functional tests for uploading composi...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2880: Modified Solid_to_Fastq's underlying perl scri...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2881: Add 2 rgenetics test files I missed for testin...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2882: Forms & request controllers   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2883: Remove a debug statement, slight cleanup.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2884: adding three LGPL ECMA script helpers for rgGR...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2885: pack the new scripts for rgenetics   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2886: remove debug and clean up genetics.py   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2887: rename composite files and rewrite the html li...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2888: moved the rgGRR svg scripts to static/scripts/...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2889: Fixes and new functional tests for uploading m...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2890: Added anchors--identified by encoded id--to da...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2891: Remove Genome Graphs and replace with topTable...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2892: Fixed a form definition editing bug   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2893: removed bogus unit tests from new gg/gff   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2894: Fix setting the peek when a line is already un...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2895: Show encoded URL, while still allowing unencod...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2896: trackster: caching goes by zoom levels, greatl...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2897: add image for trackster, use relative image ur...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2898: Changes to User Menu and History|Options menu....   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2899: Remove debugging stmt.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2900: Make HDA grid unicode compatible.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2901: revert root.py (backward compatibility issue)   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2902: Style updates to external view of history.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2903: New functional test harness. Update to recent ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2904: Don't unpack dist-eggs   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2905: Fix for tool tests. Comment out get_peek test, ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2906: Updated solid_to_fastq so that -1 qualities ar...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2907: Added a paper citation to the Bowtie wrapper t...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2908: fix dataset link that broke ucsc links   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2909: Make sqlalchemy queries use sa_session.query( ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2910: Tables for storing visualizations, visualizati...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2911: Fix for SA session when track_jobs_in_database...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2912: Some missed fixes for sqlalchemy 0.5 form of q...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2913: Fix query style in tracks controller   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2914: 2 more sqlalchemy 0.5 query fixes.   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2915: Make Galaxy attempt to honor the user's umask ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2916: Migration script for viz   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2917: trackster: fix blocks display, navigation issu...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2918: Tweaking trackster UI to fit Galaxy interface ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2919: Fixed a bug in viewing request type   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2920: Samples go to to next state when bar codes are...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2921: trackster: fix layout issue   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2922: A get_platform() monkeypatch for fat versions ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2923: Fix display of stranded features without block...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2924: Require login to perform visualization (otherw...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2925: Changed the number of threads from 8 to 4 for ...   Greg Von Kuster
• [galaxy-dev] [hg] galaxy 2926: Fix a bug whereby PYTHONPATH would grow endles...   Greg Von Kuster
• [galaxy-dev] About cluster computing support   sondos seif
• [galaxy-dev] About cluster computing support   Nate Coraor
• [galaxy-dev] bowtie and bwa   Mark Garner
• [galaxy-dev] bowtie and bwa   Kelly Vincent
• [galaxy-dev] Ease-of-Use with galaxy and workflows (long rant)   Assaf Gordon
• [galaxy-dev] Error in my functional test   Vipin Thankam Sreedharan
• [galaxy-dev] Error in my functional test   Greg Von Kuster
• [galaxy-dev] Error in my functional test   Nate Coraor
• [galaxy-dev] Error in my functional test   Vipin TS
• [galaxy-dev] Error in my functional test   Nate Coraor
• [galaxy-dev] Error in my functional test   Vipin TS
• [galaxy-dev] Error in my functional test   Nate Coraor
• [galaxy-dev] Error in my functional test   Vipin TS
• [galaxy-dev] Error in my functional test   Nate Coraor
• [galaxy-dev] Error in my functional test   Vipin TS
• [galaxy-dev] Error in my functional test   Nate Coraor
• [galaxy-dev] Error uploading file   Dijk, F van
• [galaxy-dev] Error uploading file   Nate Coraor
• [galaxy-dev] Error uploading file   Pedro Silva
• [galaxy-dev] Error uploading file   Nate Coraor
• [galaxy-dev] Error uploading file   Pedro Silva
• [galaxy-dev] Error uploading file   Nate Coraor
• [galaxy-dev] Feature request: counting job queue time   Gordon, Assaf
• [galaxy-dev] Feature request: counting job queue time   Jeremy Goecks
• [galaxy-dev] Fwd: [galaxy-user] starting workflows with a pool of input files   Matthias Dodt
• [galaxy-dev] Issue with sam_fa_indices.loc.sample   Tam, Oliver
• [galaxy-dev] Issue with sam_fa_indices.loc.sample   Kelly Vincent
• [galaxy-dev] Latest download from repository   Dijk, F van
• [galaxy-dev] Latest download from repository   Kelly Vincent
• [galaxy-dev] Library dataset upload   SHAUN WEBB
• [galaxy-dev] Library dataset upload   Nate Coraor
• [galaxy-dev] Metadata changes in workflows   Assaf Gordon
• [galaxy-dev] New tools: bigWig & bigBed   Assaf Gordon
• [galaxy-dev] New tools: bigWig & bigBed   Greg Von Kuster
• [galaxy-dev] NGS impressions (long)   Gordon, Assaf
• [galaxy-dev] NGS impressions (long)   Anton Nekrutenko
• [galaxy-dev] NGS impressions (long)   Assaf Gordon
• [galaxy-dev] NGS impressions (long)   Anton Nekrutenko
• [galaxy-dev] Problem with sqlalchemy / python versions   Assaf Gordon
• [galaxy-dev] Problem with sqlalchemy / python versions   Nate Coraor
• [galaxy-dev] Problem with sqlalchemy / python versions   Assaf Gordon
• [galaxy-dev] request: dedicated python files for user datatypes   Assaf Gordon
• [galaxy-dev] request: dedicated python files for user datatypes   Greg Von Kuster
• [galaxy-dev] Running tools on command line   SHAUN WEBB
• [galaxy-dev] Running tools on command line   Nate Coraor
• [galaxy-dev] Starting Workflow n-times   Matthias Dodt
• [galaxy-dev] tool_conf.xml question   Assaf Gordon
• [galaxy-dev] tool_conf.xml question   Anton Nekrutenko
• [galaxy-dev] toolpane info links   Gunnar Rätsch
• [galaxy-dev] Writing functional test for galaxy tool.   Vipin Thankam Sreedharan
• [galaxy-dev] Writing functional test for galaxy tool.   Greg Von Kuster
• [galaxy-dev] Writing functional test for galaxy tool.   Vipin Thankam Sreedharan

Last message date: Fri Oct 30 17:32:01 EDT 2009
Archived on: Tue Nov 10 15:15:40 EST 2009

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