Timeline



Nov 21, 2014:

2:35 PM Changeset [2968] by Nicklas Nordborg
References #696: Implement some skin examples for BASE Added "Server …
12:55 PM Changeset [2967] by Nicklas Nordborg
References #696: Implement some skin examples for BASE Added "Gold" …

Nov 20, 2014:

12:31 PM Changeset [2966] by olle
Refs #690. Since no biopsy type annotation is currently used in …
11:25 AM Changeset [2965] by olle
Refs #690. Javascript file persinfo.js in resources/personal/
9:17 AM Changeset [2964] by olle
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 Nicklas Nordborg
fixed: (In [2963]) Fixes #700: Missing '-' between plate name and library …
8:01 AM Changeset [2963] by Nicklas Nordborg
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 Nicklas Nordborg

Nov 19, 2014:

3:34 PM Changeset [2962] by olle
Refs #690. Two new sites, "Karlskrona" and "Växjö" added, both …
2:03 PM Changeset [2961] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
1:34 PM Changeset [2960] by Nicklas Nordborg
Merge Reggie 2.17.2 to trunk.
1:01 PM Changeset [2959] by Nicklas Nordborg
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 Nicklas Nordborg
Released Reggie 2.17.2 (diff)
12:56 PM reggie-2.17.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 2.17.2
12:56 PM Ticket #697 (Can't start alignment if there are libraries without a library plate) closed by Nicklas Nordborg
fixed
12:54 PM Changeset [2958] by Nicklas Nordborg
Tagging Reggie 2.17.2
12:53 PM Ticket #699 (Library registration doesn't warn about missing values in Caliper well ...) closed by Nicklas Nordborg
fixed: (In [2957]) Fixes #699: Caliper importer doesn't warn about missing …
12:53 PM Changeset [2957] by Nicklas Nordborg
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 Nicklas Nordborg
If a Caliper well table CSV file contains a row for a sample that has …
10:57 AM Changeset [2956] by Nicklas Nordborg
Preparing to release Reggie 2.17.2
10:51 AM Changeset [2955] by Nicklas Nordborg
References #697: Can't start alignment if there are libraries without …
9:27 AM Changeset [2954] by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2953]) Fixes #698: Set number of nodes in the demux wizard
8:48 AM Changeset [2953] by Nicklas Nordborg
Fixes #698: Set number of nodes in the demux wizard
8:39 AM Changeset [2952] by Nicklas Nordborg
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 Nicklas Nordborg
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 Nicklas Nordborg
The javascript is not prepared for this case since it tries to add the …

Nov 18, 2014:

1:10 PM Changeset [2951] by olle
Refs #690. Text file README updated to describe MeLuDi v.1.0-a01.
10:43 AM Changeset [2950] by olle
Refs #690. Currently unused files and directories removed (file …
10:40 AM Changeset [2949] by olle
Refs #690. Ant build file build.xml updated to not include removed …
8:46 AM Changeset [2948] by olle
Refs #690. Currently unused files and directories removed, forcing …
8:18 AM Changeset [2947] by olle
Refs #690. SVN properties svn:ignore updated/created for two …

Nov 17, 2014:

11:21 AM Changeset [2946] by olle
Refs #690. Java servlet ExportServlet removed, since it is not used …
10:00 AM Changeset [2945] by olle
Refs #690. Java classes/files updated to allow a "MeLuDi" column to …
9:52 AM Changeset [2944] by olle
Refs #690. Java servlet class/file InstallServlet.java in …
9:26 AM Changeset [2943] by Nicklas Nordborg
Merge Reggie 2.17.1 to trunk.
9:23 AM Changeset [2942] by Nicklas Nordborg
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 Nicklas Nordborg
Released Reggie 2.17.1 (diff)
9:19 AM reggie-2.17.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 2.17.1
9:18 AM Changeset [2941] by Nicklas Nordborg
Tagging Reggie 2.17.1
9:17 AM Changeset [2940] by Nicklas Nordborg
Preparing to release Reggie 2.17.1
8:48 AM Changeset [2939] by olle
Refs #690. CSS files case_summary.css and printable.css in …
8:41 AM Changeset [2938] by olle
Refs #690. Javascript file case-summary.js in resources/scripts/
8:29 AM Changeset [2937] by olle
Refs #690. Files README and RELEASE updated to refer to meludi
8:14 AM Changeset [2936] by olle
Refs #690. File LICENSE updated to refer to MeLuDi instead of Reggie.
7:45 AM Changeset [2935] by olle
Refs #690. File meludi.jar removed from source code control, since …
7:39 AM Changeset [2934] by olle
Refs #690. File json-simple-1.1.1.jar in lib/compile/ removed, …

Nov 14, 2014:

4:08 PM Changeset [2933] by olle
Refs #690. Initial check-in of source code for MeLuDi BASE extension. …
3:02 PM Changeset [2932] by Nicklas Nordborg
References #696: Implement some skin examples for BASE Initial …
1:57 PM Ticket #628 (Add right-click menu to create pools wizard) closed by Nicklas Nordborg
fixed: (In [2931]) Fixes #628: Add right-click menu to create pools wizard
1:57 PM Changeset [2931] by Nicklas Nordborg
Fixes #628: Add right-click menu to create pools wizard
1:56 PM Changeset [2930] by Nicklas Nordborg
References #672: RNA concentration normalization wizard .n instead of …
12:50 PM Changeset [2929] by Nicklas Nordborg
Adding trunk and tags to skin-collection.
12:49 PM Changeset [2928] by Nicklas Nordborg
Fixing typo.
12:49 PM Changeset [2927] by Nicklas Nordborg
Adding root folder for "Skin-collection" extension.
12:45 PM Ticket #696 (Implement some skin examples for BASE) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1886 and …
8:28 AM Ticket #695 (New reporter annotations) created by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2926]) Fixes #694: Path-element tags should use subclass instad …
8:25 AM Changeset [2926] by Nicklas Nordborg
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 Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2925]) Fixes #693: Move debug utilities to a toolbar at bottom of …
9:54 AM Changeset [2925] by Nicklas Nordborg
Fixes #693: Move debug utilities to a toolbar at bottom of page Fixed …
9:35 AM Changeset [2924] by Nicklas Nordborg
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 Nicklas Nordborg
In some wizards there are debug utilities, for example, for generating …
2:50 PM Changeset [2923] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Adding a …
9:31 AM Ticket #635 (Include analysis information in the case summary) closed by Nicklas Nordborg
fixed
9:11 AM Ticket #673 (Register RNA QC results from BioAnalyzer runs) closed by Nicklas Nordborg
fixed: (In [2922]) Fixes #673: Register RNA QC results from BioAnalyzer? runs …
9:11 AM Changeset [2922] by Nicklas Nordborg
Fixes #673: Register RNA QC results from BioAnalyzer? runs Manual …

Nov 11, 2014:

2:12 PM Changeset [2921] by Nicklas Nordborg
References #635: Include analysis information in the case summary Use …
1:53 PM Changeset [2920] by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2919]) Fixes #692: Some icons in case summary are broken in print …
1:43 PM Changeset [2919] by Nicklas Nordborg
Fixes #692: Some icons in case summary are broken in print version
1:18 PM Changeset [2918] by Nicklas Nordborg
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 Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2917]) Fixes #691: Items in case summary are not sorted Also …
12:36 PM Changeset [2917] by Nicklas Nordborg
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 Nicklas Nordborg
For some item types, there is no specific ordering if there are …
11:40 AM Changeset [2916] by Nicklas Nordborg
References #635: Include analysis information in the case summary Add …
11:13 AM Changeset [2915] by Nicklas Nordborg
References #635: Include analysis information in the case summary Add …
11:01 AM Changeset [2914] by Nicklas Nordborg
References #635: Include analysis information in the case summary …
8:29 AM Changeset [2913] by Nicklas Nordborg
References #635: Include analysis information in the case summary …
8:05 AM Changeset [2912] by Nicklas Nordborg
References #635: Include analysis information in the case summary …

Nov 10, 2014:

2:21 PM Changeset [2911] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
10:33 AM Ticket #679 (Configuration file improvments) closed by Nicklas Nordborg
fixed
10:32 AM Ticket #689 (Use new script for checking Illumina data files) closed by Nicklas Nordborg
fixed: (In [2910]) Fixes #689: Use new script for checking Illumina data …
10:32 AM Changeset [2910] by Nicklas Nordborg
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 olle
A package of registration wizards for melanoma-lung cancer projects …
8:33 AM net.sf.basedb.meludi created by olle
Initial page creation
8:09 AM Ticket #689 (Use new script for checking Illumina data files) created by Nicklas Nordborg
The picard program (see #631) mostly checks that data files exists and …

Nov 7, 2014:

2:11 PM Changeset [2909] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Add …
2:00 PM Changeset [2908] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Fixed the …
1:50 PM Changeset [2907] by Nicklas Nordborg
References #672: RNA concentration normalization wizard The rest of …
12:44 PM Changeset [2906] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Started with …
7:53 AM Changeset [2905] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Aliquots …

Nov 6, 2014:

3:49 PM Changeset [2904] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Added a count …
2:51 PM Changeset [2903] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Added "RNA …
2:06 PM net.sf.basedb.reggie/HistoryOfReggie edited by Nicklas Nordborg
Adding Reggie 2.17 sceenshot (diff)
2:05 PM reggie-2.17.png attached to net.sf.basedb.reggie/HistoryOfReggie by Nicklas Nordborg
8:12 AM Changeset [2902] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Remove …

Nov 5, 2014:

2:51 PM Changeset [2901] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Updated …
2:26 PM Changeset [2900] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Updated …
1:06 PM Changeset [2899] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Add *.r.a
1:03 PM Changeset [2898] by Nicklas Nordborg
References #672: RNA concentration normalization wizard Created new …
12:44 PM Ticket #688 (Depend on BASE 3.3.3) closed by Nicklas Nordborg
fixed: (In [2897]) Fixes #688: Depend on BASE 3.3.3
12:44 PM Changeset [2897] by Nicklas Nordborg
Fixes #688: Depend on BASE 3.3.3
12:40 PM Ticket #688 (Depend on BASE 3.3.3) created by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2896]) Fixes #687: ApWeight? field in partition wizard doesn't …
12:36 PM Changeset [2896] by Nicklas Nordborg
Fixes #687: ApWeight? field in partition wizard doesn't auto-tab on …
12:34 PM Changeset [2895] by Nicklas Nordborg
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 Nicklas Nordborg
8:47 AM Changeset [2894] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …

Nov 4, 2014:

10:09 AM Changeset [2893] by Nicklas Nordborg
References #679: Configuration file improvments Also detect …
10:00 AM Changeset [2892] by Nicklas Nordborg
References #679: Configuration file improvments Updates for better …
8:10 AM Changeset [2891] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …

Nov 3, 2014:

4:15 PM net.sf.basedb.reggie/notes217 edited by Jari Häkkinen
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 Nicklas Nordborg
Merge Reggie 2.17 to trunk.
2:53 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 2.17 (diff)
2:52 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 2.17 (diff)
2:51 PM reggie-2.17.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 2.17
2:49 PM Changeset [2889] by Nicklas Nordborg
Tagging Reggie 2.17
2:48 PM Changeset [2888] by Nicklas Nordborg
Preparing to release Reggie 2.17
2:44 PM Ticket #526 (Retraction wizard) closed by Nicklas Nordborg
fixed
2:44 PM Ticket #630 (Start cufflinks) closed by Nicklas Nordborg
fixed
2:43 PM Changeset [2887] by Nicklas Nordborg
Merge configuration file changes from 2.17-stable to trunk.
2:43 PM Ticket #686 (Limit jobs to 16 slots by default) closed by Nicklas Nordborg
fixed: (In [2886]) Fixes #686: Limit jobs to 16 slots by default
2:43 PM Changeset [2886] by Nicklas Nordborg
Fixes #686: Limit jobs to 16 slots by default
2:42 PM Ticket #686 (Limit jobs to 16 slots by default) created by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2885]) Fixes #685: New Bowtie version 2.2.4
2:40 PM Changeset [2885] by Nicklas Nordborg
Fixes #685: New Bowtie version 2.2.4
2:36 PM Ticket #685 (New Bowtie version 2.2.4) created by Nicklas Nordborg
/usr/local/packages/bowtie/2.2.4/bin/bowtie2
2:35 PM Changeset [2884] by Nicklas Nordborg
References #630: Start cufflinks Changed options for Cufflinks.
11:11 AM Changeset [2883] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
9:07 AM Ticket #642 (Confirm feature extraction as completed) closed by Nicklas Nordborg
fixed
9:06 AM Ticket #641 (Import data from cufflinks result files) closed by Nicklas Nordborg
fixed
8:32 AM Ticket #684 (Run picard AddOrReplaceReadGroups after alignment) closed by Nicklas Nordborg
fixed
8:29 AM Changeset [2882] by Nicklas Nordborg
References #684: Run picard AddOrReplaceReadGroups? after alignment …
8:24 AM Ticket #682 (Improve performance when submitting jobs to cluster) closed by Nicklas Nordborg
fixed: (In [2881]) Fixes #682: Run picard AddOrReplaceReadGroups? after …
8:24 AM Changeset [2881] by Nicklas Nordborg
Fixes #682: Run picard AddOrReplaceReadGroups? after alignment
7:55 AM Changeset [2880] by Nicklas Nordborg
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 Nicklas Nordborg
Downstream analysis tools need this information. Typical command is: …

Oct 30, 2014:

12:51 PM Changeset [2879] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
12:16 PM Changeset [2878] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
11:52 AM Changeset [2877] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
10:50 AM Changeset [2876] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
8:10 AM Changeset [2875] by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2874]) Fixes #683: Do not start processes in the background
4:28 PM Changeset [2874] by Nicklas Nordborg
Fixes #683: Do not start processes in the background
4:28 PM Ticket #683 (Do not start processes in the background) created by Nicklas Nordborg
There are a few remaining places where we start processes in the …
1:35 PM Changeset [2873] by Nicklas Nordborg
References #682: Improve performance when submitting jobs to cluster …
12:45 PM Changeset [2872] by Nicklas Nordborg
References #682: Improve performance when submitting jobs to cluster …
8:51 AM Ticket #682 (Improve performance when submitting jobs to cluster) created by Nicklas Nordborg
Submitting multiple jobs to the cluster can take a long time. For …

Oct 28, 2014:

3:31 PM Changeset [2871] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
2:44 PM Changeset [2870] by Nicklas Nordborg
References #674: Generate document with report of sequencing results …
2:43 PM net.sf.basedb.reggie edited by Nicklas Nordborg
References #676. Change license to AGPL 3 (diff)
2:37 PM Changeset [2869] by Nicklas Nordborg
References #676: Switch to AGPL v3 license Second try with only the …
2:36 PM Changeset [2868] by Nicklas Nordborg
References #676. Revert [2867] since it included changes not part of …
2:34 PM Ticket #676 (Switch to AGPL v3 license) closed by Nicklas Nordborg
fixed: (In [2867]) Fixes #676: Switch to AGPL v3 license
2:34 PM Changeset [2867] by Nicklas Nordborg
Fixes #676: Switch to AGPL v3 license
2:24 PM Changeset [2866] by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2865]) Fixes #681: Run CheckIlluminaDirectory? from a cluster node …
2:23 PM Changeset [2865] by Nicklas Nordborg
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 Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2864]) Fixes #680: Cleanup script for PostgreSQL development clone
1:01 PM Changeset [2864] by Nicklas Nordborg
Fixes #680: Cleanup script for PostgreSQL development clone
12:32 PM Ticket #680 (Cleanup script for PostgreSQL development clone) created by Nicklas Nordborg
Though I had this already, but can't find it now... The cleanup …
9:06 AM Changeset [2863] by Nicklas Nordborg
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 Nicklas Nordborg
fixed: (In [2862]) Fixes #678: Operator delivery comment in specimen tube …
7:50 AM Changeset [2862] by Nicklas Nordborg
Fixes #678: Operator delivery comment in specimen tube registration …

Oct 27, 2014:

4:20 PM Changeset [2861] by Nicklas Nordborg
References #679: Configuration file improvments Moved some …
2:10 PM Changeset [2860] by Nicklas Nordborg
References #679: Configuration file improvments Load non-grid host as …
1:22 PM Changeset [2859] by Nicklas Nordborg
References #679: Configuration file improvments Renamed configuration …
12:58 PM Ticket #679 (Configuration file improvments) created by Nicklas Nordborg
Reggie currently include a configuration file for Open Grid Scheduler …

Oct 24, 2014:

2:08 PM Ticket #678 (Operator delivery comment in specimen tube registration wizard is not saved) created by Nicklas Nordborg
It should be saved per specimen tube in the OperatorDeliveryComment
Note: See TracTimeline for information about the timeline view.