Timeline
Nov 24, 2014:
- 3:33 PM Ticket #672 (RNA concentration normalization wizard) closed by
- fixed
- 2:21 PM Changeset [2973] by
- References #674: Generate document with report of sequencing results. …
- 2:16 PM Changeset [2972] by
- References #696: Implement some skin examples for BASE Added color …
- 11:21 AM Changeset [2971] by
- References #696: Implement some skin examples for BASE Need more …
- 11:20 AM Changeset [2970] by
- References #701: Check compability with BASE 3.4 Print buttons on lab …
- 11:01 AM Ticket #702 (Use skin features in BASE 3.4) created by
- BASE 3.4 introduces the possibility to install 'skins' to change the …
- 11:00 AM Ticket #701 (Check compability with BASE 3.4) created by
- BASE 3.4 introduces the possibility to install 'skins' to change the …
- 9:27 AM Changeset [2969] by
- References #696: Implement some skin examples for BASE Added …
Nov 21, 2014:
- 2:35 PM Changeset [2968] by
- References #696: Implement some skin examples for BASE Added "Server …
- 12:55 PM Changeset [2967] by
- References #696: Implement some skin examples for BASE Added "Gold" …
Nov 20, 2014:
- 12:31 PM Changeset [2966] by
- Refs #690. Since no biopsy type annotation is currently used in …
- 11:25 AM Changeset [2965] by
-
Refs #690. Javascript file
persinfo.jsinresources/personal/… - 9:17 AM Changeset [2964] by
- Refs #690. The case registration section is updated with an initial …
- 8:01 AM Ticket #700 (Missing '-' between plate name and library name in start alignment and ...) closed by
- fixed: (In [2963]) Fixes #700: Missing '-' between plate name and library …
- 8:01 AM Changeset [2963] by
- Fixes #700: Missing '-' between plate name and library name in start …
- 7:59 AM Ticket #700 (Missing '-' between plate name and library name in start alignment and ...) created by
Nov 19, 2014:
- 3:34 PM Changeset [2962] by
- Refs #690. Two new sites, "Karlskrona" and "Växjö" added, both …
- 2:03 PM Changeset [2961] by
- References #674: Generate document with report of sequencing results …
- 1:34 PM Changeset [2960] by
- Merge Reggie 2.17.2 to trunk.
- 1:01 PM Changeset [2959] by
- Preparing for future release Reggie 2.17.3
- 12:59 PM Milestone Reggie v2.17.2 completed
- Bug fixes for Reggie 2.17.1. See [wiki:net.sf.basedb.reggie Reggie …
- 12:57 PM net.sf.basedb.reggie edited by
- Released Reggie 2.17.2 (diff)
- 12:56 PM Ticket #697 (Can't start alignment if there are libraries without a library plate) closed by
- fixed
- 12:54 PM Changeset [2958] by
- Tagging Reggie 2.17.2
- 12:53 PM Ticket #699 (Library registration doesn't warn about missing values in Caliper well ...) closed by
- fixed: (In [2957]) Fixes #699: Caliper importer doesn't warn about missing …
- 12:53 PM Changeset [2957] by
- Fixes #699: Caliper importer doesn't warn about missing values in …
- 11:58 AM Ticket #699 (Library registration doesn't warn about missing values in Caliper well ...) created by
- If a Caliper well table CSV file contains a row for a sample that has …
- 10:57 AM Changeset [2956] by
- Preparing to release Reggie 2.17.2
- 10:51 AM Changeset [2955] by
- References #697: Can't start alignment if there are libraries without …
- 9:27 AM Changeset [2954] by
- References #697: Can't start alignment if there are libraries without …
- 8:48 AM Ticket #698 (Set number of nodes in the demux wizard) closed by
- fixed: (In [2953]) Fixes #698: Set number of nodes in the demux wizard
- 8:48 AM Changeset [2953] by
- Fixes #698: Set number of nodes in the demux wizard
- 8:39 AM Changeset [2952] by
- References #697: Can't start alignment if there are libraries without …
- 7:52 AM Ticket #698 (Set number of nodes in the demux wizard) created by
- The number of nodes to use for a demux job is currently configured in …
- 7:49 AM Ticket #697 (Can't start alignment if there are libraries without a library plate) created by
- The javascript is not prepared for this case since it tries to add the …
Nov 18, 2014:
- 1:10 PM Changeset [2951] by
-
Refs #690. Text file
READMEupdated to describe MeLuDi v.1.0-a01. - 10:43 AM Changeset [2950] by
- Refs #690. Currently unused files and directories removed (file …
- 10:40 AM Changeset [2949] by
-
Refs #690. Ant build file
build.xmlupdated to not include removed … - 8:46 AM Changeset [2948] by
- Refs #690. Currently unused files and directories removed, forcing …
- 8:18 AM Changeset [2947] by
- Refs #690. SVN properties svn:ignore updated/created for two …
Nov 17, 2014:
- 11:21 AM Changeset [2946] by
-
Refs #690. Java servlet
ExportServletremoved, since it is not used … - 10:00 AM Changeset [2945] by
-
Refs #690. Java classes/files updated to allow a "
MeLuDi" column to … - 9:52 AM Changeset [2944] by
-
Refs #690. Java servlet class/file
InstallServlet.javain … - 9:26 AM Changeset [2943] by
- Merge Reggie 2.17.1 to trunk.
- 9:23 AM Changeset [2942] by
- Preparing for future release Reggie 2.17.2
- 9:21 AM Milestone Reggie v2.17.1 completed
- Bug fixes for Reggie 2.17. See [wiki:net.sf.basedb.reggie Reggie …
- 9:21 AM net.sf.basedb.reggie edited by
- Released Reggie 2.17.1 (diff)
- 9:18 AM Changeset [2941] by
- Tagging Reggie 2.17.1
- 9:17 AM Changeset [2940] by
- Preparing to release Reggie 2.17.1
- 8:48 AM Changeset [2939] by
-
Refs #690. CSS files
case_summary.cssandprintable.cssin … - 8:41 AM Changeset [2938] by
-
Refs #690. Javascript file
case-summary.jsinresources/scripts/… - 8:29 AM Changeset [2937] by
-
Refs #690. Files
READMEandRELEASEupdated to refer tomeludi… - 8:14 AM Changeset [2936] by
-
Refs #690. File
LICENSEupdated to refer toMeLuDiinstead ofReggie. - 7:45 AM Changeset [2935] by
-
Refs #690. File
meludi.jarremoved from source code control, since … - 7:39 AM Changeset [2934] by
-
Refs #690. File
json-simple-1.1.1.jarinlib/compile/removed, …
Nov 14, 2014:
- 4:08 PM Changeset [2933] by
- Refs #690. Initial check-in of source code for MeLuDi BASE extension. …
- 3:02 PM Changeset [2932] by
- References #696: Implement some skin examples for BASE Initial …
- 1:57 PM Ticket #628 (Add right-click menu to create pools wizard) closed by
- fixed: (In [2931]) Fixes #628: Add right-click menu to create pools wizard
- 1:57 PM Changeset [2931] by
- Fixes #628: Add right-click menu to create pools wizard
- 1:56 PM Changeset [2930] by
- References #672: RNA concentration normalization wizard .n instead of …
- 12:50 PM Changeset [2929] by
- Adding trunk and tags to skin-collection.
- 12:49 PM Changeset [2928] by
- Fixing typo.
- 12:49 PM Changeset [2927] by
- Adding root folder for "Skin-collection" extension.
- 12:45 PM Ticket #696 (Implement some skin examples for BASE) created by
- See http://base.thep.lu.se/ticket/1886 and …
- 8:28 AM Ticket #695 (New reporter annotations) created by
- The default GTF file we use (UCSC_hg38_knownGenes_22sep2014.gtf) has …
- 8:25 AM Ticket #694 (Path-element tags should use subclass instad of clazz) closed by
- fixed: (In [2926]) Fixes #694: Path-element tags should use subclass instad …
- 8:25 AM Changeset [2926] by
- Fixes #694: Path-element tags should use subclass instad of clazz
- 8:22 AM Ticket #694 (Path-element tags should use subclass instad of clazz) created by
- The case summary page uses clazz which effectively replaces the …
Nov 13, 2014:
- 9:54 AM Ticket #693 (Move debug utilities to a toolbar at bottom of page) closed by
- fixed: (In [2925]) Fixes #693: Move debug utilities to a toolbar at bottom of …
- 9:54 AM Changeset [2925] by
- Fixes #693: Move debug utilities to a toolbar at bottom of page Fixed …
- 9:35 AM Changeset [2924] by
- References #693: Move debug utilities to a toolbar at bottom of page …
Nov 12, 2014:
- 2:55 PM Ticket #693 (Move debug utilities to a toolbar at bottom of page) created by
- In some wizards there are debug utilities, for example, for generating …
- 2:50 PM Changeset [2923] by
- References #672: RNA concentration normalization wizard Adding a …
- 9:31 AM Ticket #635 (Include analysis information in the case summary) closed by
- fixed
- 9:11 AM Ticket #673 (Register RNA QC results from BioAnalyzer runs) closed by
- fixed: (In [2922]) Fixes #673: Register RNA QC results from BioAnalyzer? runs …
- 9:11 AM Changeset [2922] by
- Fixes #673: Register RNA QC results from BioAnalyzer? runs Manual …
Nov 11, 2014:
- 2:12 PM Changeset [2921] by
- References #635: Include analysis information in the case summary Use …
- 1:53 PM Changeset [2920] by
- References #689: Use new script for checking Illumina data files …
- 1:43 PM Ticket #692 (Some icons in case summary are broken in print version) closed by
- fixed: (In [2919]) Fixes #692: Some icons in case summary are broken in print …
- 1:43 PM Changeset [2919] by
- Fixes #692: Some icons in case summary are broken in print version
- 1:18 PM Changeset [2918] by
- References #635: Include analysis information in the case summary …
- 1:16 PM Ticket #692 (Some icons in case summary are broken in print version) created by
- For example, PDF file icons linked from some bioplates (eg. mRNA plate).
- 12:36 PM Ticket #691 (Items in case summary are not sorted) closed by
- fixed: (In [2917]) Fixes #691: Items in case summary are not sorted Also …
- 12:36 PM Changeset [2917] by
- Fixes #691: Items in case summary are not sorted Also added …
- 12:00 PM Ticket #691 (Items in case summary are not sorted) created by
- For some item types, there is no specific ordering if there are …
- 11:40 AM Changeset [2916] by
- References #635: Include analysis information in the case summary Add …
- 11:13 AM Changeset [2915] by
- References #635: Include analysis information in the case summary Add …
- 11:01 AM Changeset [2914] by
- References #635: Include analysis information in the case summary …
- 8:29 AM Changeset [2913] by
- References #635: Include analysis information in the case summary …
- 8:05 AM Changeset [2912] by
- References #635: Include analysis information in the case summary …
Nov 10, 2014:
- 2:21 PM Changeset [2911] by
- References #674: Generate document with report of sequencing results …
- 10:33 AM Ticket #679 (Configuration file improvments) closed by
- fixed
- 10:32 AM Ticket #689 (Use new script for checking Illumina data files) closed by
- fixed: (In [2910]) Fixes #689: Use new script for checking Illumina data …
- 10:32 AM Changeset [2910] by
- Fixes #689: Use new script for checking Illumina data files It is now …
- 9:57 AM Ticket #690 (MeLuDi - Registration wizard for melanoma-lung cancer projects) created by
- A package of registration wizards for melanoma-lung cancer projects …
- 8:33 AM net.sf.basedb.meludi created by
- Initial page creation
- 8:09 AM Ticket #689 (Use new script for checking Illumina data files) created by
- The picard program (see #631) mostly checks that data files exists and …
Nov 7, 2014:
- 2:11 PM Changeset [2909] by
- References #672: RNA concentration normalization wizard Add …
- 2:00 PM Changeset [2908] by
- References #672: RNA concentration normalization wizard Fixed the …
- 1:50 PM Changeset [2907] by
- References #672: RNA concentration normalization wizard The rest of …
- 12:44 PM Changeset [2906] by
- References #672: RNA concentration normalization wizard Started with …
- 7:53 AM Changeset [2905] by
- References #672: RNA concentration normalization wizard Aliquots …
Nov 6, 2014:
- 3:49 PM Changeset [2904] by
- References #672: RNA concentration normalization wizard Added a count …
- 2:51 PM Changeset [2903] by
- References #672: RNA concentration normalization wizard Added "RNA …
- 2:06 PM net.sf.basedb.reggie/HistoryOfReggie edited by
- Adding Reggie 2.17 sceenshot (diff)
- 8:12 AM Changeset [2902] by
- References #672: RNA concentration normalization wizard Remove …
Nov 5, 2014:
- 2:51 PM Changeset [2901] by
- References #672: RNA concentration normalization wizard Updated …
- 2:26 PM Changeset [2900] by
- References #672: RNA concentration normalization wizard Updated …
- 1:06 PM Changeset [2899] by
-
References #672: RNA concentration normalization wizard
Add
*.r.a… - 1:03 PM Changeset [2898] by
- References #672: RNA concentration normalization wizard Created new …
- 12:44 PM Ticket #688 (Depend on BASE 3.3.3) closed by
- fixed: (In [2897]) Fixes #688: Depend on BASE 3.3.3
- 12:44 PM Changeset [2897] by
- Fixes #688: Depend on BASE 3.3.3
- 12:40 PM Ticket #688 (Depend on BASE 3.3.3) created by
- The 'Start feature extraction' wizard doesn't work very well without …
- 12:36 PM Ticket #687 (ApWeight field in partition wizard doesn't auto-tab on ENTER key) closed by
- fixed: (In [2896]) Fixes #687: ApWeight? field in partition wizard doesn't …
- 12:36 PM Changeset [2896] by
- Fixes #687: ApWeight? field in partition wizard doesn't auto-tab on …
- 12:34 PM Changeset [2895] by
- Changes for future release Reggie 2.17.1
- 11:37 AM Ticket #687 (ApWeight field in partition wizard doesn't auto-tab on ENTER key) created by
- 8:47 AM Changeset [2894] by
- References #674: Generate document with report of sequencing results …
Nov 4, 2014:
- 10:09 AM Changeset [2893] by
- References #679: Configuration file improvments Also detect …
- 10:00 AM Changeset [2892] by
- References #679: Configuration file improvments Updates for better …
- 8:10 AM Changeset [2891] by
- References #674: Generate document with report of sequencing results …
Nov 3, 2014:
- 4:15 PM net.sf.basedb.reggie/notes217 edited by
- Fixing spelling (diff)
- 2:59 PM Milestone Reggie v2.17 completed
- Focus on completing the "Secondary analysis" wizards. See …
- 2:59 PM Changeset [2890] by
- Merge Reggie 2.17 to trunk.
- 2:53 PM PluginDownload edited by
- Released Reggie 2.17 (diff)
- 2:52 PM net.sf.basedb.reggie edited by
- Released Reggie 2.17 (diff)
- 2:49 PM Changeset [2889] by
- Tagging Reggie 2.17
- 2:48 PM Changeset [2888] by
- Preparing to release Reggie 2.17
- 2:44 PM Ticket #526 (Retraction wizard) closed by
- fixed
- 2:44 PM Ticket #630 (Start cufflinks) closed by
- fixed
- 2:43 PM Changeset [2887] by
- Merge configuration file changes from 2.17-stable to trunk.
- 2:43 PM Ticket #686 (Limit jobs to 16 slots by default) closed by
- fixed: (In [2886]) Fixes #686: Limit jobs to 16 slots by default
- 2:43 PM Changeset [2886] by
- Fixes #686: Limit jobs to 16 slots by default
- 2:42 PM Ticket #686 (Limit jobs to 16 slots by default) created by
- The current configuration have no upper limit for the number of slots …
- 2:40 PM Ticket #685 (New Bowtie version 2.2.4) closed by
- fixed: (In [2885]) Fixes #685: New Bowtie version 2.2.4
- 2:40 PM Changeset [2885] by
- Fixes #685: New Bowtie version 2.2.4
- 2:36 PM Ticket #685 (New Bowtie version 2.2.4) created by
- /usr/local/packages/bowtie/2.2.4/bin/bowtie2
- 2:35 PM Changeset [2884] by
- References #630: Start cufflinks Changed options for Cufflinks.
- 11:11 AM Changeset [2883] by
- References #674: Generate document with report of sequencing results …
- 9:07 AM Ticket #642 (Confirm feature extraction as completed) closed by
- fixed
- 9:06 AM Ticket #641 (Import data from cufflinks result files) closed by
- fixed
- 8:32 AM Ticket #684 (Run picard AddOrReplaceReadGroups after alignment) closed by
- fixed
- 8:29 AM Changeset [2882] by
- References #684: Run picard AddOrReplaceReadGroups? after alignment …
- 8:24 AM Ticket #682 (Improve performance when submitting jobs to cluster) closed by
- fixed: (In [2881]) Fixes #682: Run picard AddOrReplaceReadGroups? after …
- 8:24 AM Changeset [2881] by
- Fixes #682: Run picard AddOrReplaceReadGroups? after alignment
- 7:55 AM Changeset [2880] by
- References #640: Finalize update to new scripting pattern Code for …
Oct 31, 2014:
- 11:43 AM Ticket #684 (Run picard AddOrReplaceReadGroups after alignment) created by
- Downstream analysis tools need this information. Typical command is: …
Oct 30, 2014:
- 12:51 PM Changeset [2879] by
- References #674: Generate document with report of sequencing results …
- 12:16 PM Changeset [2878] by
- References #674: Generate document with report of sequencing results …
- 11:52 AM Changeset [2877] by
- References #674: Generate document with report of sequencing results …
- 10:50 AM Changeset [2876] by
- References #674: Generate document with report of sequencing results …
- 8:10 AM Changeset [2875] by
- References #679: Configuration file improvments Fixes an issue with …
Oct 29, 2014:
- 4:28 PM Ticket #683 (Do not start processes in the background) closed by
- fixed: (In [2874]) Fixes #683: Do not start processes in the background
- 4:28 PM Changeset [2874] by
- Fixes #683: Do not start processes in the background
- 4:28 PM Ticket #683 (Do not start processes in the background) created by
- There are a few remaining places where we start processes in the …
- 1:35 PM Changeset [2873] by
- References #682: Improve performance when submitting jobs to cluster …
- 12:45 PM Changeset [2872] by
- References #682: Improve performance when submitting jobs to cluster …
- 8:51 AM Ticket #682 (Improve performance when submitting jobs to cluster) created by
- Submitting multiple jobs to the cluster can take a long time. For …
Oct 28, 2014:
- 3:31 PM Changeset [2871] by
- References #674: Generate document with report of sequencing results …
- 2:44 PM Changeset [2870] by
- References #674: Generate document with report of sequencing results …
- 2:43 PM net.sf.basedb.reggie edited by
- References #676. Change license to AGPL 3 (diff)
- 2:37 PM Changeset [2869] by
- References #676: Switch to AGPL v3 license Second try with only the …
- 2:36 PM Changeset [2868] by
- References #676. Revert [2867] since it included changes not part of …
- 2:34 PM Ticket #676 (Switch to AGPL v3 license) closed by
- fixed: (In [2867]) Fixes #676: Switch to AGPL v3 license
- 2:34 PM Changeset [2867] by
- Fixes #676: Switch to AGPL v3 license
- 2:24 PM Changeset [2866] by
- References #681: Run CheckIlluminaDirectory? from a cluster node …
- 2:23 PM Ticket #681 (Run CheckIlluminaDirectory from a cluster node instead of the cluster ...) closed by
- fixed: (In [2865]) Fixes #681: Run CheckIlluminaDirectory? from a cluster node …
- 2:23 PM Changeset [2865] by
- Fixes #681: Run CheckIlluminaDirectory? from a cluster node instead of …
- 1:43 PM Ticket #681 (Run CheckIlluminaDirectory from a cluster node instead of the cluster ...) created by
- It is not very nice to use the main controller to run the …
- 1:01 PM Ticket #680 (Cleanup script for PostgreSQL development clone) closed by
- fixed: (In [2864]) Fixes #680: Cleanup script for PostgreSQL development clone
- 1:01 PM Changeset [2864] by
- Fixes #680: Cleanup script for PostgreSQL development clone
- 12:32 PM Ticket #680 (Cleanup script for PostgreSQL development clone) created by
- Though I had this already, but can't find it now... The cleanup …
- 9:06 AM Changeset [2863] by
- References #674: Generate document with report of sequencing results …
- 7:50 AM Ticket #678 (Operator delivery comment in specimen tube registration wizard is not saved) closed by
- fixed: (In [2862]) Fixes #678: Operator delivery comment in specimen tube …
- 7:50 AM Changeset [2862] by
- Fixes #678: Operator delivery comment in specimen tube registration …
Oct 27, 2014:
- 4:20 PM Changeset [2861] by
- References #679: Configuration file improvments Moved some …
- 2:10 PM Changeset [2860] by
- References #679: Configuration file improvments Load non-grid host as …
- 1:22 PM Changeset [2859] by
- References #679: Configuration file improvments Renamed configuration …
- 12:58 PM Ticket #679 (Configuration file improvments) created by
- Reggie currently include a configuration file for Open Grid Scheduler …
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