Timeline
Nov 6, 2014:
- 3:49 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2904]) References #672: RNA concentration normalization wizard …
- 3:49 PM Changeset [2904] by
- References #672: RNA concentration normalization wizard Added a count …
- 2:51 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2903]) References #672: RNA concentration normalization wizard …
- 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 Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2902]) References #672: RNA concentration normalization wizard …
- 8:12 AM Changeset [2902] by
- References #672: RNA concentration normalization wizard Remove …
Nov 5, 2014:
- 2:51 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2901]) References #672: RNA concentration normalization wizard …
- 2:51 PM Changeset [2901] by
- References #672: RNA concentration normalization wizard Updated …
- 2:26 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2900]) References #672: RNA concentration normalization wizard …
- 2:26 PM Changeset [2900] by
- References #672: RNA concentration normalization wizard Updated …
- 1:06 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2899]) References #672: RNA concentration normalization wizard …
- 1:06 PM Changeset [2899] by
-
References #672: RNA concentration normalization wizard
Add
*.r.a… - 1:03 PM Ticket #672 (RNA concentration normalization wizard) updated by
- (In [2898]) References #672: RNA concentration normalization wizard …
- 1:03 PM Changeset [2898] by
- References #672: RNA concentration normalization wizard Created new …
- 12:47 PM Ticket #672 (RNA concentration normalization wizard) updated by
-
Status changed
- 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
- 11:53 AM Ticket #672 (RNA concentration normalization wizard) updated by
-
Description, Summary changed
- 11:39 AM Ticket #687 (ApWeight field in partition wizard doesn't auto-tab on ENTER key) updated by
-
Status, Milestone changed
- 11:37 AM Ticket #687 (ApWeight field in partition wizard doesn't auto-tab on ENTER key) created by
- 8:47 AM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2894]) References #674: Generate document with report of …
- 8:47 AM Changeset [2894] by
- References #674: Generate document with report of sequencing results …
Nov 4, 2014:
- 10:09 AM Ticket #679 (Configuration file improvments) updated by
- (In [2893]) References #679: Configuration file improvments Also …
- 10:09 AM Changeset [2893] by
- References #679: Configuration file improvments Also detect …
- 10:00 AM Ticket #679 (Configuration file improvments) updated by
- (In [2892]) References #679: Configuration file improvments Updates …
- 10:00 AM Changeset [2892] by
- References #679: Configuration file improvments Updates for better …
- 8:10 AM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2891]) References #674: Generate document with report of …
- 8:10 AM Changeset [2891] by
- References #674: Generate document with report of sequencing results …
- 8:00 AM Ticket #679 (Configuration file improvments) updated by
-
Status changed
- 8:00 AM Ticket #674 (Generate document with report of sequencing results) updated by
-
Status changed
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 Ticket #630 (Start cufflinks) updated by
- (In [2884]) References #630: Start cufflinks Changed options for …
- 2:35 PM Changeset [2884] by
- References #630: Start cufflinks Changed options for Cufflinks.
- 2:26 PM Ticket #673 (Register RNA QC results from BioAnalyzer runs) updated by
-
Status changed
- 11:11 AM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2883]) References #674: Generate document with report of …
- 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
- 8:30 AM Ticket #684 (Run picard AddOrReplaceReadGroups after alignment) updated by
- (In [2881]) Fixes #684: Run picard AddOrReplaceReadGroups after alignment
- 8:29 AM Ticket #684 (Run picard AddOrReplaceReadGroups after alignment) updated by
- (In [2882]) References #684: Run picard AddOrReplaceReadGroups after …
- 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 Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2880]) References #640: Finalize update to new scripting pattern …
- 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 Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2879]) References #674: Generate document with report of …
- 12:51 PM Changeset [2879] by
- References #674: Generate document with report of sequencing results …
- 12:16 PM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2878]) References #674: Generate document with report of …
- 12:16 PM Changeset [2878] by
- References #674: Generate document with report of sequencing results …
- 11:52 AM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2877]) References #674: Generate document with report of …
- 11:52 AM Changeset [2877] by
- References #674: Generate document with report of sequencing results …
- 10:50 AM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2876]) References #674: Generate document with report of …
- 10:50 AM Changeset [2876] by
- References #674: Generate document with report of sequencing results …
- 8:10 AM Ticket #679 (Configuration file improvments) updated by
- (In [2875]) References #679: Configuration file improvments Fixes an …
- 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 Ticket #682 (Improve performance when submitting jobs to cluster) updated by
- (In [2873]) References #682: Improve performance when submitting jobs …
- 1:35 PM Changeset [2873] by
- References #682: Improve performance when submitting jobs to cluster …
- 12:45 PM Ticket #682 (Improve performance when submitting jobs to cluster) updated by
- (In [2872]) References #682: Improve performance when submitting jobs …
- 12:45 PM Changeset [2872] by
- References #682: Improve performance when submitting jobs to cluster …
- 9:24 AM Ticket #682 (Improve performance when submitting jobs to cluster) updated by
-
Further investigations:
* Batching all
rmandmkdirinto one SSH … - 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 Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2871]) References #674: Generate document with report of …
- 3:31 PM Changeset [2871] by
- References #674: Generate document with report of sequencing results …
- 2:44 PM Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2870]) References #674: Generate document with report of …
- 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 Ticket #676 (Switch to AGPL v3 license) updated by
- (In [2869]) References #676: Switch to AGPL v3 license Second try …
- 2:37 PM Changeset [2869] by
- References #676: Switch to AGPL v3 license Second try with only the …
- 2:36 PM Ticket #676 (Switch to AGPL v3 license) updated by
- (In [2868]) References #676. Revert [2867] since it included changes …
- 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 Ticket #681 (Run CheckIlluminaDirectory from a cluster node instead of the cluster ...) updated by
- (In [2866]) References #681: Run CheckIlluminaDirectory from a cluster …
- 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 Ticket #674 (Generate document with report of sequencing results) updated by
- (In [2863]) References #674: Generate document with report of …
- 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 Ticket #679 (Configuration file improvments) updated by
- (In [2861]) References #679: Configuration file improvments Moved …
- 4:20 PM Changeset [2861] by
- References #679: Configuration file improvments Moved some …
- 2:10 PM Ticket #679 (Configuration file improvments) updated by
- (In [2860]) References #679: Configuration file improvments Load …
- 2:10 PM Changeset [2860] by
- References #679: Configuration file improvments Load non-grid host as …
- 1:22 PM Ticket #679 (Configuration file improvments) updated by
- (In [2859]) References #679: Configuration file improvments Renamed …
- 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 Ticket #641 (Import data from cufflinks result files) updated by
- (In [2856]) References #641: Import data from cufflinks result files …
- 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
- 11:13 AM Ticket #676 (Switch to AGPL v3 license) updated by
-
Description changed
- 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 Ticket #641 (Import data from cufflinks result files) updated by
- (In [2851]) References #641: Import data from cufflinks result files …
- 12:31 PM Changeset [2851] by
- References #641: Import data from cufflinks result files chromosome …
- 9:20 AM Ticket #630 (Start cufflinks) updated by
- (In [2850]) References #630 (and #675): Start cufflinks Adding …
- 9:20 AM Changeset [2850] by
- References #630 (and #675): Start cufflinks Adding support for just …
- 8:51 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) updated by
- (In [2849]) References #675: Running a mask/align job as debug for a …
- 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 …
- 8:09 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) updated by
- I think there are two things that should be fixed: * Add -u …
- 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 Ticket #630 (Start cufflinks) updated by
- (In [2847]) References #630: Start cufflinks Re-organized …
- 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 Ticket #526 (Retraction wizard) updated by
- (In [2845]) References #526: Retraction wizard Remove unused imports.
- 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!
- 8:08 AM Ticket #642 (Confirm feature extraction as completed) updated by
-
Status changed
- 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:
- 4:09 PM Ticket #526 (Retraction wizard) updated by
- (In [2841). Refs #526. …
- 4:00 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2842]) References #640: Finalize update to new scripting pattern …
- 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 Ticket #526 (Retraction wizard) updated by
- (In [2839]) Refs #526. First version of the retraction wizard, that …
- 2:25 PM Changeset [2839] by
- Refs #526. First version of the retraction wizard, that lists data for …
- 1:47 PM Ticket #650 (New type of specimen core biopsy) updated by
-
Status, Milestone changed
- 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
- 1:35 PM Ticket #651 (Add 1x16 pool schema to create mRNA plate wizard) updated by
-
Status changed
- 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
- 11:22 AM Ticket #638 (Fix issues with not filling all pools on a a plate) updated by
-
Milestone, Status changed
- 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 #669 (RNAQC Caliper well table import wizard should check if values are missing) updated by
-
Status changed
- 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 Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2834]) References #640: Finalize update to new scripting pattern …
- 9:26 AM Changeset [2834] by
- References #640: Finalize update to new scripting pattern Setting …
- 9:19 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2833]) References #640: Finalize update to new scripting pattern …
- 9:19 AM Changeset [2833] by
- References #640: Finalize update to new scripting pattern Removing …
- 9:16 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2832]) References #640: Finalize update to new scripting pattern …
- 9:16 AM Changeset [2832] by
- References #640: Finalize update to new scripting pattern Updated the …
Oct 17, 2014:
- 4:11 PM Ticket #526 (Retraction wizard) updated by
- Design specification: The code design borrows (steals) heavily from …
- 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 Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2829]) References #640: Finalize update to new scripting pattern …
- 9:34 AM Changeset [2829] by
- References #640: Finalize update to new scripting pattern Updated the …
Oct 16, 2014:
- 3:43 PM Ticket #642 (Confirm feature extraction as completed) updated by
- (In [2828]) References #642: Confirm feature extraction as completed …
- 3:43 PM Changeset [2828] by
- References #642: Confirm feature extraction as completed New file …
- 3:40 PM Ticket #668 (Cache result of queries used to count items on Reggie index page) closed by
- fixed: (In [2827]) Fixes #668: Cache result of queries used to count items on …
- 3:40 PM Changeset [2827] by
- Fixes #668: Cache result of queries used to count items on Reggie …
- 2:56 PM Ticket #642 (Confirm feature extraction as completed) updated by
- (In [2826]) References #642: Confirm feature extraction as completed …
- 2:56 PM Changeset [2826] by
- References #642: Confirm feature extraction as completed Started with …
- 1:45 PM Ticket #668 (Cache result of queries used to count items on Reggie index page) created by
- Some of the (oldest) queries do this, but as new wizards has been …
- 12:41 PM Changeset [2825] by
- Merge Reggie 2.16.3 to the trunk.
- 12:39 PM Changeset [2824] by
- Preparing for future release Reggie 2.16.4
- 12:37 PM Milestone Reggie v2.16.3 completed
- Bug fixes for Reggie 2.16.2. See [wiki:net.sf.basedb.reggie Reggie …
- 12:36 PM PluginDownload edited by
- Released Reggie 2.16.3 (diff)
- 12:36 PM net.sf.basedb.reggie edited by
- Released Reggie 2.16.3 (diff)
- 12:34 PM Changeset [2823] by
- Tagging Reggie 2.16.3
- 12:33 PM Changeset [2822] by
- Preparing to release Reggie 2.16.3
- 11:58 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) closed by
- fixed: (In [2821]) Fixes #667: Library registration wizard complains about …
- 11:58 AM Changeset [2821] by
- Fixes #667: Library registration wizard complains about missing …
- 11:55 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) updated by
- Seems like this was caused by changes in [2675] when trying to improve …
- 11:12 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) updated by
- (In [2820]) References #667: Library registration wizard complains …
- 11:12 AM Changeset [2820] by
- References #667: Library registration wizard complains about missing …
- 10:58 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) updated by
- First thing I noticed is that the 'generate fake file' feature that is …
- 10:55 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) created by
- The qubit and caliper files seems to be ok, but the library …
- 9:50 AM Changeset [2819] by
- Merge Reggie 2.16.2 to the trunk.
- 9:46 AM Changeset [2818] by
- Preparing for future release Reggie 2.16.3
- 9:45 AM Milestone Reggie v2.16.2 completed
- Bug fixes for Reggie 2.16.1. See [wiki:net.sf.basedb.reggie Reggie …
- 9:44 AM PluginDownload edited by
- Released Reggie 2.16.2 (diff)
- 9:44 AM net.sf.basedb.reggie edited by
- Released Reggie 2.16.2 (diff)
- 9:41 AM Changeset [2817] by
- Tagging Reggie 2.16.2
- 9:40 AM Changeset [2816] by
- Preparing to release Reggie 2.16.2
- 9:38 AM Ticket #665 (Display pool name in warning messages) closed by
- fixed: (In [2815]) Fixes #665: Display pool name in warning messages
- 9:38 AM Changeset [2815] by
- Fixes #665: Display pool name in warning messages
- 9:35 AM Ticket #666 (Default number of slots for demux should be 4) updated by
- (In [2814]) References #666: Default number of slots for demux should …
- 9:35 AM Changeset [2814] by
- References #666: Default number of slots for demux should be 4 Same …
- 9:34 AM Ticket #666 (Default number of slots for demux should be 4) closed by
- fixed: (In [2813]) Fixes #666: Default number of slots for demux should be 4
- 9:34 AM Changeset [2813] by
- Fixes #666: Default number of slots for demux should be 4
- 9:33 AM Ticket #666 (Default number of slots for demux should be 4) created by
- Tests have shown that this is good enough and leaves a lot of other …
- 9:14 AM Ticket #664 (Display pool names in confirm demux wizard) closed by
- fixed: (In [2812]) Fixes #664: Display pool names in confirm demux wizard …
- 9:14 AM Changeset [2812] by
- Fixes #664: Display pool names in confirm demux wizard Additional …
- 8:07 AM Ticket #665 (Display pool name in warning messages) created by
- […]
- 8:05 AM Ticket #664 (Display pool names in confirm demux wizard) created by
- 8:04 AM Ticket #663 (Demux script should not gzip FASTQ files until the last step) closed by
- fixed: (In [2811]) Fixes #663: Demux script should not gzip FASTQ files until …
- 8:04 AM Changeset [2811] by
- Fixes #663: Demux script should not gzip FASTQ files until the last step
Oct 15, 2014:
- 3:27 PM Ticket #662 (Race conditions in demux script) closed by
- fixed: (In [2810]) Fixes #662: Race conditions in demux script This was …
- 3:27 PM Changeset [2810] by
- Fixes #662: Race conditions in demux script This was caused by …
- 2:59 PM Ticket #663 (Demux script should not gzip FASTQ files until the last step) created by
- This currently happens when merging the FASTQ files from the demux. …
- 2:56 PM Ticket #662 (Race conditions in demux script) created by
- The demux script starts some of the steps in the background, but there …
- 2:07 PM Ticket #630 (Start cufflinks) updated by
- (In [2809]) References #630: Start cufflinks Must wait for the fix …
- 2:07 PM Changeset [2809] by
- References #630: Start cufflinks Must wait for the fix commands to …
- 1:18 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2808]) References #640: Finalize update to new scripting pattern …
- 1:18 PM Changeset [2808] by
- References #640: Finalize update to new scripting pattern Changes …
- 1:11 PM Ticket #630 (Start cufflinks) updated by
- (In [2807]) References #630: Start cufflinks Added option to select …
- 1:11 PM Changeset [2807] by
- References #630: Start cufflinks Added option to select an import …
- 10:29 AM Ticket #630 (Start cufflinks) updated by
- (In [2806]) References #630: Start cufflinks New tracking-id mapping …
- 10:29 AM Changeset [2806] by
- References #630: Start cufflinks New tracking-id mapping file that is …
- 9:39 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2805]) References #640: Finalize update to new scripting pattern …
- 9:39 AM Changeset [2805] by
- References #640: Finalize update to new scripting pattern Updated the …
Oct 14, 2014:
- 3:44 PM Ticket #661 (Calculate average fragment size and standard deviation after tophat) closed by
- fixed: (In [2804]) Fixes #661: Calculate average fragment size and standard …
- 3:44 PM Changeset [2804] by
- Fixes #661: Calculate average fragment size and standard deviation …
- 2:12 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2803]) References #640: Finalize update to new scripting pattern …
- 2:12 PM Changeset [2803] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:32 AM Ticket #661 (Calculate average fragment size and standard deviation after tophat) created by
- This is the same as we already do in the demux step. But in this case …
Oct 13, 2014:
- 2:52 PM Ticket #656 (FASTQ files are not always stored in the expected folder) updated by
- (In [2802]) References #656: FASTQ files are not always stored in the …
- 2:52 PM Changeset [2802] by
- References #656: FASTQ files are not always stored in the expected …
- 2:49 PM Changeset [2801] by
- Merge Reggie 2.16.1 to the trunk.
- 2:39 PM Changeset [2800] by
- Preparing for future release Reggie 2.16.2
- 2:39 PM PluginDownload edited by
- Released Reggie 2.16.1 (diff)
- 2:37 PM Milestone Reggie v2.16.1 completed
- Bug fixes for Reggie 2.16. See [wiki:net.sf.basedb.reggie Reggie …
- 2:36 PM net.sf.basedb.reggie edited by
- Released Reggie 2.16.1 (diff)
- 2:33 PM Changeset [2799] by
- Tagging Reggie 2.16.1
- 2:32 PM Changeset [2798] by
- Preparing to release Reggie 2.16.1
- 2:30 PM Ticket #660 (Error in sample source report wizard) closed by
- fixed: (In [2797]) Fixes #660: Error in sample source report wizard
- 2:30 PM Changeset [2797] by
- Fixes #660: Error in sample source report wizard
- 2:26 PM Ticket #660 (Error in sample source report wizard) created by
- Go to the sample source report wizard. Select the 'Overview report' …
- 1:32 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2796]) References #640: Finalize update to new scripting pattern …
- 1:32 PM Changeset [2796] by
- References #640: Finalize update to new scripting pattern Found some …
- 1:31 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2795]) References #640: Finalize update to new scripting pattern …
- 1:31 PM Changeset [2795] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:32 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2794]) References #640: Finalize update to new scripting pattern …
- 11:32 AM Changeset [2794] by
- References #640: Finalize update to new scripting pattern Updated the …
- 9:38 AM Changeset [2793] by
- Synchronize changes from #653, #654, #658 and #659 to the trunk.
- 9:27 AM Ticket #657 (Include Reggie version number in wizards) updated by
- (In [2792]) References #657: Include Reggie version number in wizards …
- 9:27 AM Changeset [2792] by
- References #657: Include Reggie version number in wizards Added …
- 9:18 AM Ticket #659 (Do not trust fragement size calculated by bowtie if number of used ...) closed by
- fixed: (In [2791]) Fixes #659: Do not trust fragement size calculated by …
- 9:18 AM Changeset [2791] by
- Fixes #659: Do not trust fragement size calculated by bowtie if number …
- 9:14 AM Ticket #657 (Include Reggie version number in wizards) updated by
- (In [2790]) References #657: Include Reggie version number in wizards …
- 9:14 AM Changeset [2790] by
- References #657: Include Reggie version number in wizards Change …
- 9:12 AM Changeset [2789] by
- Oh, that's just my pet snake, Reggie!
- 8:54 AM Ticket #659 (Do not trust fragement size calculated by bowtie if number of used ...) created by
-
The
FragmentSizeAvgandFragmentSizeStdshould be set to -1 if the … - 8:51 AM Ticket #658 (Adjust fragment size mean and standard deviation) closed by
- fixed: (In [2788]) Fixes #658: Adjust fragment size mean and standard …
- 8:51 AM Changeset [2788] by
- Fixes #658: Adjust fragment size mean and standard deviation Added …
- 8:41 AM Ticket #653 (Use explicit paths to all important program used in pipeline) updated by
- (In [2787]) References #653: Use explicit paths to all important …
- 8:41 AM Changeset [2787] by
- References #653: Use explicit paths to all important program used in …
- 7:42 AM Ticket #653 (Use explicit paths to all important program used in pipeline) updated by
- (In [2786]) References #653: Use explicit paths to all important …
- 7:42 AM Changeset [2786] by
- References #653: Use explicit paths to all important program used in …
Oct 10, 2014:
- 3:27 PM Ticket #658 (Adjust fragment size mean and standard deviation) updated by
-
Description changed
- 2:23 PM Ticket #658 (Adjust fragment size mean and standard deviation) created by
- In the demux step we introduced a call to bowtie that is used to …
- 12:59 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2785]) References #640: Finalize update to new scripting pattern …
- 12:59 PM Changeset [2785] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:55 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2784]) References #640: Finalize update to new scripting pattern …
- 11:55 AM Changeset [2784] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:14 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2783]) References #640: Finalize update to new scripting pattern …
- 11:14 AM Changeset [2783] by
- References #640: Finalize update to new scripting pattern Updated the …
- 10:59 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2782]) References #640: Finalize update to new scripting pattern …
- 10:59 AM Changeset [2782] by
- References #640: Finalize update to new scripting pattern Updated the …
- 9:17 AM Changeset [2781] by
- Tag mismatch.
- 9:14 AM Ticket #657 (Include Reggie version number in wizards) closed by
- fixed: (In [2780]) Fixes #657: Include Reggie version number in wizards …
- 9:14 AM Changeset [2780] by
- Fixes #657: Include Reggie version number in wizards build.xml …
- 9:11 AM Ticket #657 (Include Reggie version number in wizards) created by
- 8:27 AM Ticket #656 (FASTQ files are not always stored in the expected folder) closed by
- fixed: (In [2779]) Fixes #656: FASTQ files are not always stored in the …
- 8:27 AM Changeset [2779] by
- Fixes #656: FASTQ files are not always stored in the expected folder …
Oct 9, 2014:
- 12:42 PM Changeset [2778] by
- 12:41 PM Changeset [2777] by
- 12:41 PM Changeset [2776] by
- 12:32 PM Changeset [2775] by
- Registration extension for Melanoma/Lung cancer project.
- 11:39 AM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2774]) References #640: Finalize update to new scripting pattern …
- 11:39 AM Changeset [2774] by
- References #640: Finalize update to new scripting pattern Updated the …
- 8:40 AM Ticket #656 (FASTQ files are not always stored in the expected folder) updated by
- (In [2773]) References #656: FASTQ files are not always stored in the …
- 8:40 AM Changeset [2773] by
- References #656: FASTQ files are not always stored in the expected …
- 8:13 AM Ticket #654 (Synchronize default options for pipeline analysis) closed by
- fixed
- 8:13 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2772]) References #654: Synchronize default options for pipeline …
- 8:13 AM Changeset [2772] by
- References #654: Synchronize default options for pipeline analysis …
- 8:10 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2771]) References #654: Synchronize default options for pipeline …
- 8:10 AM Changeset [2771] by
- References #654: Synchronize default options for pipeline analysis …
- 8:09 AM Ticket #655 (PT_READS is not reported correctly in description for FASTQ files) closed by
- fixed: (In [2770]) Fixes #655: PT_READS is not reported correctly in …
- 8:09 AM Changeset [2770] by
- Fixes #655: PT_READS is not reported correctly in description for …
Oct 8, 2014:
- 9:46 PM Ticket #656 (FASTQ files are not always stored in the expected folder) created by
- Expected: […] Actual: […] This difference is also mapped to …
- 9:41 PM Ticket #655 (PT_READS is not reported correctly in description for FASTQ files) created by
- For example: 30803478 READS; 30803478 PF_READS; [J@11c2cada PT_READS
- 12:51 PM Ticket #653 (Use explicit paths to all important program used in pipeline) closed by
- fixed: (In [2769]) Fixes #653: Use explicit paths to all important program …
- 12:51 PM Changeset [2769] by
- Fixes #653: Use explicit paths to all important program used in …
- 11:59 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2768]) References #654: Synchronize default options for pipeline …
- 11:59 AM Changeset [2768] by
- References #654: Synchronize default options for pipeline analysis …
- 11:52 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2767]) References #654: Synchronize default options for pipeline …
- 11:52 AM Changeset [2767] by
- References #654: Synchronize default options for pipeline analysis …
- 11:49 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2766]) References #654: Synchronize default options for pipeline …
- 11:49 AM Changeset [2766] by
- References #654: Synchronize default options for pipeline analysis …
- 11:48 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2765]) References #654: Synchronize default options for pipeline …
- 11:48 AM Changeset [2765] by
- References #654: Synchronize default options for pipeline analysis …
- 11:45 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2764]) References #654: Synchronize default options for pipeline …
- 11:45 AM Changeset [2764] by
- References #654: Synchronize default options for pipeline analysis …
- 11:43 AM Ticket #654 (Synchronize default options for pipeline analysis) updated by
- (In [2763]) References #654: Synchronize default options for pipeline …
- 11:43 AM Changeset [2763] by
- References #654: Synchronize default options for pipeline analysis …
- 11:42 AM Ticket #654 (Synchronize default options for pipeline analysis) created by
- The reggie-ogs-hosts.xml file contain a lot of options for the …
- 11:40 AM Ticket #653 (Use explicit paths to all important program used in pipeline) updated by
- (In [2762]) References #653: Use explicit paths to all important …
- 11:40 AM Changeset [2762] by
- References #653: Use explicit paths to all important program used in …
- 11:37 AM Ticket #653 (Use explicit paths to all important program used in pipeline) created by
- Eg. Tophat and bowtie. It is already possible to set a path in the …
- 9:40 AM Ticket #652 (New location of BASE JAR files) closed by
- fixed: I guess that should be most of the BASE3-compatible plug-ins/extensions.
- 9:37 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2761]) References #652: New location of BASE JAR files YubiKey trunk.
- 9:37 AM Changeset [2761] by
- References #652: New location of BASE JAR files YubiKey trunk.
- 9:35 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2760]) References #652: New location of BASE JAR files X-files trunk.
- 9:35 AM Changeset [2760] by
- References #652: New location of BASE JAR files X-files trunk.
- 9:34 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2759]) References #652: New location of BASE JAR files …
- 9:34 AM Changeset [2759] by
- References #652: New location of BASE JAR files Normalizers trunk.
- 9:33 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2758]) References #652: New location of BASE JAR files MeV trunk.
- 9:33 AM Changeset [2758] by
- References #652: New location of BASE JAR files MeV trunk.
- 9:32 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2757]) References #652: New location of BASE JAR files LabEnv trunk.
- 9:32 AM Changeset [2757] by
- References #652: New location of BASE JAR files LabEnv trunk.
- 9:31 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2756]) References #652: New location of BASE JAR files Illumina …
- 9:31 AM Changeset [2756] by
- References #652: New location of BASE JAR files Illumina plug-ins trunk.
- 9:29 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2755]) References #652: New location of BASE JAR files HDFS trunk.
- 9:29 AM Changeset [2755] by
- References #652: New location of BASE JAR files HDFS trunk.
- 9:27 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2754]) References #652: New location of BASE JAR files Code …
- 9:27 AM Changeset [2754] by
- References #652: New location of BASE JAR files Code examples trunk.
- 9:26 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2753]) References #652: New location of BASE JAR files FTP …
- 9:26 AM Changeset [2753] by
- References #652: New location of BASE JAR files FTP Server trunk.
- 9:24 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2752]) References #652: New location of BASE JAR files Reggie …
- 9:24 AM Changeset [2752] by
- References #652: New location of BASE JAR files Reggie trunk. But …
- 9:24 AM Ticket #652 (New location of BASE JAR files) updated by
- (In [2751]) References #652: New location of BASE JAR files Reggie …
- 9:23 AM Changeset [2751] by
- References #652: New location of BASE JAR files Reggie 2.16-stable.
- 9:20 AM Ticket #652 (New location of BASE JAR files) created by
- This affects all plug-ins that has implemented automatic download of …
- 9:12 AM Ticket #630 (Start cufflinks) updated by
- (In [2750]) References #630: Start cufflinks Added support for …
- 9:12 AM Changeset [2750] by
- References #630: Start cufflinks Added support for re-mapping some …
- 9:07 AM Ticket #640 (Finalize update to new scripting pattern) updated by
-
Status changed
- 9:06 AM Changeset [2749] by
- Adding script for replacing tracking_id values in the fpkm_tracking …
- 8:43 AM Ticket #651 (Add 1x16 pool schema to create mRNA plate wizard) created by
- This schema is likely going to be used in the future. It may not …
- 8:35 AM Ticket #650 (New type of specimen core biopsy) created by
- Taken between the first core biopsy and the operator. Referral form …
- 8:35 AM Ticket #526 (Retraction wizard) updated by
- Functional specification: The first version of the retraction wizard …
- 8:17 AM Ticket #649 (Better balance in progress when demuxing) closed by
- fixed: (In [2748]) Fixes #649: Better balance in progress when demuxing
- 8:17 AM Changeset [2748] by
- Fixes #649: Better balance in progress when demuxing
- 8:14 AM Ticket #649 (Better balance in progress when demuxing) created by
- The current implementation assigns 50% of the progress to the demux …
Oct 7, 2014:
- 2:45 PM Ticket #641 (Import data from cufflinks result files) updated by
- (In [2747]) References #641: Import data from cufflinks result files …
- 2:45 PM Changeset [2747] by
- References #641: Import data from cufflinks result files Adding …
- 12:36 PM Ticket #646 (New options for specimen type in specimen tube registration) closed by
- fixed: (In [2746]) Fixes #646: New options for specimen type in specimen tube …
- 12:36 PM Changeset [2746] by
- Fixes #646: New options for specimen type in specimen tube registration
- 12:32 PM Ticket #646 (New options for specimen type in specimen tube registration) reopened by
- 12:32 PM Ticket #640 (Finalize update to new scripting pattern) updated by
- (In [2745]) References #640: Finalize update to new scripting pattern …
- 12:32 PM Changeset [2745] by
- References #640: Finalize update to new scripting pattern More …
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