May 2010 Archives by author

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Starting: Mon May 10 11:58:52 EDT 2010
Ending: Tue May 25 08:53:53 EDT 2010
Messages: 158

• [galaxy-commits] [hg] galaxy 3663: Fix issue where you cannot expand datasets in ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3665: Add GTF file format to Galaxy. GTF format is a...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3664: Complete Cufflinks wrapper.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3666: Add column join tool to main tool conf   Nate Coraor
• [galaxy-commits] [hg] galaxy 3667: Fix autocomplete for Edit Attributes dbkeys   Nate Coraor
• [galaxy-commits] [hg] galaxy 3668: User-custom dbkeys can now be set for datasets...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3670: Make failing to load datatype converters and d...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3669: Cuffcompare wrapper.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3671: Fix ordering in display_structured, also use i...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3672: GFF to Bed converter now converts the spaces t...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3673: Fix history renaming on Saved Histories grid   Nate Coraor
• [galaxy-commits] [hg] galaxy 3674: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3675: Enable the the grid helper and base grid templ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3676: Cufflinks tools update; added cuffdiff wrapper.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3677: fixed the amqp config bug   Nate Coraor
• [galaxy-commits] [hg] galaxy 3678: lims: fixed data transfer bugs   Nate Coraor
• [galaxy-commits] [hg] galaxy 3679: Fix various trackster issues   Nate Coraor
• [galaxy-commits] [hg] galaxy 3680: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3681: GTF to BEDGraph converter.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3682: lims: added request_types permissions   Nate Coraor
• [galaxy-commits] [hg] galaxy 3683: Updates for 'Profile Annotations for a set of ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3684: Community upload functionality   Nate Coraor
• [galaxy-commits] [hg] galaxy 3685: lims: add tests for request_type permissions   Nate Coraor
• [galaxy-commits] [hg] galaxy 3686: Miscellaneous community space fixes.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3687: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3688: Add categories to the community app   Nate Coraor
• [galaxy-commits] [hg] galaxy 3689: Move setting categories to the Tool class in t...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3690: Added missing templates   Nate Coraor
• [galaxy-commits] [hg] galaxy 3691: Some fixes for the async datasource tool contr...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3692: Better labels for rna-seq tools' output datasets.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3693: Fix multiple issues for history display. Fixes...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3694: Add missing job_id substitutions to jobs/runne...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3695: Rollback display links/peek ordering in histor...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3696: Fix indentations.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3697: Community app: Add the "view tool" interface a...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3698: Community space fixes and enhancements: separa...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3699: Rename the tool_browser controller and add a l...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3700: Encode HDA id for edit link in history panel.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3701: Add eland and elandmulti formats. Enhance MACs...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3702: Fix managing tool categories and separate the ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3703: Encode HDA id in Edit Attributes form.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3704: Rollback to unencoded HDAs.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3705: Fixes for viewing and editing tool info.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3706: Eliminate pop-up menu items from grid columns ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3707: Adding new regional variation tools developed ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3708: hotfix history rename   Nate Coraor
• [galaxy-commits] [hg] galaxy 3709: Reports: fixed missing 'cookie-path' settings....   Nate Coraor
• [galaxy-commits] [hg] galaxy 3710: More fixes and cleanup for the community space...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3711: A few grid hacks and community tool browser en...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3712: Allow automatic creation of GALAXY_URL for 'da...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3713: Community: Display tool tarball contents on th...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3714: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3715: Another rev on cuffcompare wrapper.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3716: trackster: BAM display supports paired-end rea...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3718: Fix for backwards compatibility of HDAs being ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3717: Full Tophat wrapper. All options are implement...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3720: Remove headers from SAM file so that output ma...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3719: Make GTF type subclass from GFF type.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3721: merge   Nate Coraor
• [galaxy-commits] [hg] galaxy 3722: Many fixes and additional features added to th...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3723: Add a link to the user's uploaded tools from t...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3724: Change the way size of output file determined ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3726: Community: Add tool versioning and tighten up ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3725: Fix dbkey setting for BWA.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3727: Cuffcompare wrapper handles all outputs gracef...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3728: merge   Nate Coraor
• [galaxy-commits] [hg] galaxy 3729: Bug fixes for history import: (a) import can n...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3730: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3731: forms default value bug fixed   Nate Coraor
• [galaxy-commits] [hg] galaxy 3732: Enable viewing of shared/accessible/published ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3733: Pack scripts.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3734: Community: add help for tool-related operations   Nate Coraor
• [galaxy-commits] [hg] galaxy 3735: Enable users not logged in to view a shared/ac...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3737: Add a tip to the upload tool about using url p...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3736: Very basic support for exporting and importing...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3738: trackster: add filled line display   Nate Coraor
• [galaxy-commits] [hg] galaxy 3739: Update types for cuffcompare output files.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3740: Secure=True by default for workflows.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3741: Fix the recentrly introduced grid filter / sea...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3742: trackster: fix BAM data error; display tweaks   Nate Coraor
• [galaxy-commits] [hg] galaxy 3743: Removing debugging msg.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3744: Fix bug that mucked up fetch for chrom lengths...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3745: Enhanced column join to allow user to specify ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3746: Fix for downloading a library dataset from the...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3747: lims: workflow selectbox in the samples page f...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3748: Update documentation in cufftools wrappers.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3749: Updated builds.txt (and manual_builds.txt) to ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3750: trackster:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3751: Fix bug that was preventing annotation of work...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3752: Add the modENCODEfly and modENCODEworm data so...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3753: Fix grid filtering bug.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3754: Replace large selects w/o refresh_on_change wi...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3755: Another update to search+select: pack script a...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3756: trackster: fix track saving   Nate Coraor
• [galaxy-commits] [hg] galaxy 3757: Clean up annotation display for workflow steps.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3758: lims:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3759: SNP/WGA tool changes only   Nate Coraor
• [galaxy-commits] [hg] galaxy 3760: Add external metadata to SGE   Nate Coraor
• [galaxy-commits] [hg] galaxy 3762: Revert inadvertantly updated tool_conf.xml.sam...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3761: Bug in SGE external metadata   Nate Coraor
• [galaxy-commits] [hg] galaxy 3763: right welcome.html at last   Nate Coraor
• [galaxy-commits] [hg] galaxy 3764: Add 'filter transcripts via tracking' tool to ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3765: Remove builds.txt from source control - use bu...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3767: Add worker threads to SGE runner   Nate Coraor
• [galaxy-commits] [hg] galaxy 3768: Add mimetypes to snp/wga datatypes in genetics.py   Nate Coraor
• [galaxy-commits] [hg] galaxy 3769: Hack to fix the ghost broken dataset problem a...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3770: work around for composite objects without a ba...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3771: Fixes for uploading a tool to the community sp...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3772: Enable viewing of datasets via history/view wh...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3773: Fix buildbot's builds.txt   Nate Coraor
• [galaxy-commits] [hg] galaxy 3774: Fixes for displaying appropriate datasets in G...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3775: Force modENCODE worm dbkey to be ce6 and modEN...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3776: Remove the hack I just committed for changing ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3777: Several Fixes for Uploading Composite datatype...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3778: trackster:   Nate Coraor
• [galaxy-commits] [hg] galaxy 3779: Fix for changing a library dataset's data type...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3780: Fix for issue where connecting to a Workflow S...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3781: Only use search+select when jquery autocomplet...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3782: Fix for editing category information in the co...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3783: Add track definition to bedgraph files generat...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3785: Fix comment.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3784: Add GFF filtering tool. Tool filters GFF file ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3786: Use PBS exit_status (if keep_completed is set)...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3787: Fixes for editing tool information and submitt...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3788: Enable images and binary datasets to work with...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3789: Better UI flow for changing an HDA's data type.   Nate Coraor
• [galaxy-commits] [hg] galaxy 3790: Replace big selects that refresh on change wit...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3791: Added ldIndep datatype to genetics.py and data...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3792: More tweaks to some snp/wga composite output t...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3793: Removed redundant code from rgEigPCA.py now th...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3794: eeesh. hgignore for welcome.html didn't   Nate Coraor
• [galaxy-commits] [hg] galaxy 3795: Once more with even more feeling - welcome.htm...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3796: Added ldindep datatype to datatypes sample   Nate Coraor
• [galaxy-commits] [hg] galaxy 3797: added more options to the sff converter tool   Nate Coraor
• [galaxy-commits] [hg] galaxy 3798: add multiprocess.sh example script for running...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3799: Unreverted js changes from JG - for some stran...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3800: Enable display framework to handle unicode cha...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3801: First pass at adding Ensembl browsers as an ex...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3802: Another pass on search+select for autocomplete...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3803: Add a tool to mask FASTQ bases according to qu...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3804: Backed out changeset 48432330228e. pbs_python...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3805: merge backout   Nate Coraor
• [galaxy-commits] [hg] galaxy 3806: Require 2 paths for rgtest.sh   Nate Coraor
• [galaxy-commits] [hg] galaxy 3807: Require two paths for rgtest.sh galaxyroot and...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3808: Branch merge   Nate Coraor
• [galaxy-commits] [hg] galaxy 3809: branch merge again?   Nate Coraor
• [galaxy-commits] [hg] galaxy 3810: In Page editor, prevent extra paragraphs from ...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3811: Send the web freamework ( trans ) to the grid'...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3812: First pass at implementing a method for allowi...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3813: Added nginx mod_zip support for library downloads   Nate Coraor
• [galaxy-commits] [hg] galaxy 3814: Page editor: fix indenting issue for webkit br...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3815: Minor cleanup for ensembl display applications...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3816: sff_converter tool functional test   Nate Coraor
• [galaxy-commits] [hg] galaxy 3817: fixed the status message box layout in grid   Nate Coraor
• [galaxy-commits] [hg] galaxy 3818: Allow FASTQ Groomer/parser to work on tab-deli...   Nate Coraor
• [galaxy-commits] [hg] galaxy 3819: lims: ui fixes in adding samples   Nate Coraor
• [galaxy-commits] [hg] galaxy 3820: Committed mod_zip code from the wrong repo   Nate Coraor
• [galaxy-commits] [hg] galaxy 3766: Fix for exporting workflows with input dataset...   James Taylor

Last message date: Tue May 25 08:53:53 EDT 2010
Archived on: Tue May 25 09:06:26 EDT 2010

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