Timeline
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 …
Oct 24, 2014:
- 2:08 PM Ticket #678 (Operator delivery comment in specimen tube registration wizard is not saved) created by
-
It should be saved per specimen tube in the
OperatorDeliveryComment…
Oct 23, 2014:
- 11:24 AM Changeset [2858] by
- Changes for future Reggie 2.18
- 11:23 AM Changeset [2857] by
- Creating 2.17-stable branch for final 2.17 development.
- 11:18 AM Changeset [2856] by
- References #641: Import data from cufflinks result files …
- 11:17 AM Ticket #677 (ant 'clean' should delete downloaded BASE JAR files) closed by
- fixed: (In [2855]) Fixes #677: ant 'clean' should delete downloaded BASE JAR …
- 11:17 AM Changeset [2855] by
- Fixes #677: ant 'clean' should delete downloaded BASE JAR files
- 11:03 AM net.sf.basedb.reggie edited by
- (diff)
- 11:01 AM net.sf.basedb.reggie/HistoryOfReggie edited by
- Add release dates (diff)
- 10:02 AM net.sf.basedb.reggie/HistoryOfReggie edited by
- (diff)
- 9:53 AM net.sf.basedb.reggie/HistoryOfReggie created by
- 8:40 AM net.sf.basedb.reggie/notes217 created by
- 8:29 AM net.sf.basedb.reggie edited by
- Released Reggie 2.17-beta-1 (diff)
- 8:26 AM Ticket #677 (ant 'clean' should delete downloaded BASE JAR files) created by
- A common problem is that when Reggie moves on to depend on a newer …
- 8:22 AM Changeset [2854] by
- Tagging Reggie 2.17-beta-1
- 8:20 AM Changeset [2853] by
- Preparing to release Reggie 2.17-beta-1
Oct 22, 2014:
- 6:56 PM Changeset [2852] by
- Ignore .project file from Eclipse.
- 4:02 PM Ticket #676 (Switch to AGPL v3 license) created by
- The PDF generating library (http://www.itextpdf.com/) that we plan to …
- 12:31 PM Changeset [2851] by
- References #641: Import data from cufflinks result files chromosome …
- 9:20 AM Changeset [2850] by
- References #630 (and #675): Start cufflinks Adding support for just …
- 8:51 AM Changeset [2849] by
- References #675: Running a mask/align job as debug for a non-debug …
- 8:47 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) closed by
- fixed: (In [2848]) Fixes #675: Running a mask/align job as debug for a …
- 8:47 AM Changeset [2848] by
- Fixes #675: Running a mask/align job as debug for a non-debug demux …
- 8:05 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) created by
- The help text for the debug option says: When running in debug …
- 8:01 AM Changeset [2847] by
- References #630: Start cufflinks Re-organized configuration parameter …
Oct 21, 2014:
- 2:21 PM Ticket #674 (Generate document with report of sequencing results) created by
- When the secondary analysis pipeline has been completed we should have …
- 2:16 PM Ticket #673 (Register RNA QC results from BioAnalyzer runs) created by
- The "Create aliquots on BioAnalyzer/Caliper plates" wizard have …
- 2:11 PM Ticket #672 (RNA concentration normalization wizard) created by
- A new step that is performed immediately after RNA extraction and …
- 1:43 PM Changeset [2846] by
- Oh, that's just my pet snake, Reggie!
- 1:35 PM Changeset [2845] by
- References #526: Retraction wizard Remove unused imports.
- 1:33 PM Changeset [2844] by
- Oh, that's just my pet snake, Reggie!
- 8:07 AM Ticket #671 (Save reggie version with jobs) closed by
- fixed: (In [2843]) Fixes #671: Save reggie version with jobs
- 8:07 AM Changeset [2843] by
- Fixes #671: Save reggie version with jobs
- 7:58 AM Ticket #671 (Save reggie version with jobs) created by
- Will be possible in BASE 3.3.2 http://base.thep.lu.se/ticket/1871
Oct 20, 2014:
- 4:00 PM Changeset [2842] by
- References #640: Finalize update to new scripting pattern Found a few …
- 3:55 PM Changeset [2841] by
-
Refs 526. Servlet class/file
RetractionFormServlet.javain … - 3:41 PM Ticket #650 (New type of specimen core biopsy) closed by
- fixed: (In [2840]) Fixes #650: New type of specimen core biopsy
- 3:41 PM Changeset [2840] by
- Fixes #650: New type of specimen core biopsy
- 2:25 PM Changeset [2839] by
- Refs #526. First version of the retraction wizard, that lists data for …
- 1:47 PM Ticket #651 (Add 1x16 pool schema to create mRNA plate wizard) closed by
- fixed: (In [2838]) Fixes #651: Add 1x16 pool schema to create mRNA plate wizard
- 1:47 PM Changeset [2838] by
- Fixes #651: Add 1x16 pool schema to create mRNA plate wizard
- 1:34 PM Ticket #638 (Fix issues with not filling all pools on a a plate) closed by
- fixed: (In [2837]) Fixes #638: Fix issues with not filling all pools on a a plate
- 1:34 PM Changeset [2837] by
- Fixes #638: Fix issues with not filling all pools on a a plate
- 11:21 AM Ticket #669 (RNAQC Caliper well table import wizard should check if values are missing) closed by
- fixed: (In [2836]) Fixes #669: RNAQC Caliper well table import wizard should …
- 11:21 AM Changeset [2836] by
- Fixes #669: RNAQC Caliper well table import wizard should check if …
- 10:44 AM Ticket #670 (Echo commands used for tophat, etc to *.out files) closed by
- fixed: (In [2835]) Fixes #670: Echo commands used for tophat, etc to *.out files
- 10:44 AM Changeset [2835] by
- Fixes #670: Echo commands used for tophat, etc to *.out files
- 9:36 AM Ticket #670 (Echo commands used for tophat, etc to *.out files) created by
- Eg: […]
- 9:28 AM Ticket #640 (Finalize update to new scripting pattern) closed by
- fixed
- 9:26 AM Changeset [2834] by
- References #640: Finalize update to new scripting pattern Setting …
- 9:19 AM Changeset [2833] by
- References #640: Finalize update to new scripting pattern Removing …
- 9:16 AM Changeset [2832] by
- References #640: Finalize update to new scripting pattern Updated the …
Oct 17, 2014:
- 1:57 PM Ticket #669 (RNAQC Caliper well table import wizard should check if values are missing) created by
- The well table file from caliper is supposed to contain RQS values for …
- 11:43 AM Changeset [2831] by
- New version from Christian. added proper argument/option handling; …
- 11:37 AM Changeset [2830] by
- Print integers as integers.
- 9:34 AM Changeset [2829] by
- References #640: Finalize update to new scripting pattern Updated the …
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