Timeline


and

Sep 26, 2014:

2:06 PM net.sf.basedb.reggie edited by nicklas
(diff)
2:03 PM reggie-2.16-beta-4.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16-beta-4
2:03 PM Changeset [2703] by nicklas
Tagging Reggie 2.16-beta-4 (second try)
2:02 PM Changeset [2702] by nicklas
Resetting debug flags.
1:59 PM Changeset [2701] by nicklas
Removed since I forgot to reset debug flags.
1:43 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16-beta-4 (diff)
1:41 PM Changeset [2700] by nicklas
Tagging Reggie 2.16-beta-4
1:38 PM Changeset [2699] by nicklas
Preparing to release Reggie 2.16-beta-4

Sep 25, 2014:

12:48 PM Changeset [2698] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:47 AM Changeset [2697] by nicklas
References #593: Start masking and alignment Adding …
9:24 AM Changeset [2696] by nicklas
Adding script for fixing the unmapped.bam file generated by tophat so …

Sep 24, 2014:

4:34 PM Changeset [2695] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
4:21 PM Changeset [2694] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
4:13 PM Changeset [2693] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
1:22 PM Changeset [2692] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:30 PM Changeset [2691] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:53 AM Ticket #637 (Add annotations for lot numbers in the DNA/RNA/FlowThrough registration) closed by nicklas
fixed: (In [2690]) Fixes #637: Add annotations for lot numbers in the …
9:53 AM Changeset [2690] by nicklas
Fixes #637: Add annotations for lot numbers in the DNA/RNA/FlowThrough …

Sep 23, 2014:

3:40 PM Changeset [2689] by nicklas
References #547: Start Demux and Merge Splitting Trimmomatic into two …
12:56 PM Changeset [2688] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 22, 2014:

9:02 AM Changeset [2687] by nicklas
References #637: Add annotations for lot numbers in the …
8:30 AM Changeset [2686] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 19, 2014:

2:44 PM Ticket #638 (Fix issues with not filling all pools on a a plate) created by nicklas
For testing and evaluation purposes it is sometimes desirable to …
7:58 AM Changeset [2685] by nicklas
References #595: Confirm alignment Same change as [2683] for the …

Sep 18, 2014:

4:03 PM Changeset [2684] by nicklas
References #593: Start masking and alignment Use the average fragment …
2:37 PM Changeset [2683] by nicklas
References #548: Register Demux and Merge as ended Also delete file …
1:36 PM Changeset [2682] by nicklas
References #548: Register Demux and Merge as ended Display calculated …
11:22 AM Changeset [2681] by nicklas
References #548: Register Demux and Merge as ended Selecting …
11:19 AM Changeset [2680] by nicklas
References #547: Start Demux and Merge Calling bowtie to align a …
11:13 AM Changeset [2679] by nicklas
Adding script for calculating average of fragment lengths.
8:04 AM Changeset [2678] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 17, 2014:

4:09 PM Changeset [2677] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
10:49 AM Changeset [2676] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
10:04 AM Ticket #637 (Add annotations for lot numbers in the DNA/RNA/FlowThrough registration) created by nicklas
We would like to keep track of the lot numbers for some reagents used …
9:47 AM Changeset [2675] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 16, 2014:

2:28 PM Ticket #636 (INCA export may fail if there are blood samples with missing date) closed by nicklas
fixed: (In [2674]) Fixes #636: INCA export may fail if there are blood …
2:28 PM Changeset [2674] by nicklas
Fixes #636: INCA export may fail if there are blood samples with …
1:18 PM Ticket #636 (INCA export may fail if there are blood samples with missing date) created by nicklas
The INCA export fail in this scenario: * "all" option is selected * …
8:48 AM Changeset [2673] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
7:52 AM Changeset [2672] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
7:49 AM Changeset [2671] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 15, 2014:

4:05 PM Ticket #635 (Include analysis information in the case summary) created by nicklas
The case summary currently goes down to 'Sequencing run' items. We …
4:00 PM Ticket #634 (Retraction wizard) closed by olle
duplicate: This ticket turned out to be a duplicate of Ticket #526 "Retraction …
3:54 PM Changeset [2670] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
3:47 PM Changeset [2669] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
2:47 PM Changeset [2668] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
1:10 PM Changeset [2667] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:48 PM Changeset [2666] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:21 PM Ticket #634 (Retraction wizard) created by olle
A wizard should be created to support retraction of data for a …
9:00 AM Changeset [2665] by nicklas
Fixed incorrect message.
8:23 AM Changeset [2664] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 12, 2014:

3:03 PM Ticket #631 (Add data check to the confirm sequencing ended wizard) closed by nicklas
fixed
2:35 PM Changeset [2663] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
2:14 PM Changeset [2662] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:36 PM Ticket #633 (Adapter peak fraction=0 is displayed as 'unknown' in the pooling wizard) closed by nicklas
fixed: (In [2661]) Fixes #633: Adapter peak fraction=0 is displayed as …
12:36 PM Changeset [2661] by nicklas
Fixes #633: Adapter peak fraction=0 is displayed as 'unknown' in the …
12:29 PM Ticket #632 (Increase max volume limit in pooling wizard to 20µl) closed by nicklas
fixed: (In [2660]) Fixes #632: Increase max volume limit in pooling wizard to 20µl
12:29 PM Changeset [2660] by nicklas
Fixes #632: Increase max volume limit in pooling wizard to 20µl
12:25 PM Ticket #633 (Adapter peak fraction=0 is displayed as 'unknown' in the pooling wizard) created by nicklas
12:24 PM Ticket #632 (Increase max volume limit in pooling wizard to 20µl) created by nicklas
10:33 AM Changeset [2659] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:59 AM net.sf.basedb.labenv edited by jari
(diff)
9:05 AM Changeset [2658] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 11, 2014:

3:40 PM Changeset [2657] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
3:23 PM Changeset [2656] by nicklas
Resetting all debug flags.
3:18 PM Changeset [2655] by nicklas
References #547: Start Demux and Merge Reset the AutoProcessing
3:14 PM Changeset [2654] by nicklas
References #547: Start Demux and Merge Added 'ulimit' option for the …
2:23 PM Changeset [2653] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
11:25 AM Changeset [2652] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 10, 2014:

2:07 PM Changeset [2651] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
1:57 PM Changeset [2650] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:33 PM Changeset [2649] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:58 AM Changeset [2648] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
8:58 AM Changeset [2647] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
8:55 AM Changeset [2646] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
8:18 AM Changeset [2645] by nicklas
References #631: Add data check to the confirm sequencing ended wizard …

Sep 9, 2014:

4:03 PM net.sf.basedb.yubikey/install edited by nicklas
The yubikey-extended-properties.xml is part of the release since … (diff)
1:43 PM Changeset [2644] by nicklas
References #595: Confirm alignment The 'View remote files' dialog now …
1:33 PM Changeset [2643] by nicklas
References #631: Add data check to the confirm sequencing ended wizard …
1:28 PM Changeset [2642] by nicklas
References #631: Add data check to the confirm sequencing ended wizard …
11:38 AM Changeset [2641] by nicklas
References #631: Add data check to the confirm sequencing ended wizard …
11:31 AM Ticket #631 (Add data check to the confirm sequencing ended wizard) created by nicklas
Picard has a tool called CheckIlluminaDirectory which can be used …

Sep 8, 2014:

11:00 AM Changeset [2640] by nicklas
References #548: Register Demux and Merge as ended Added an option to …
10:42 AM Changeset [2639] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …

Sep 4, 2014:

11:14 AM Ticket #630 (Start cufflinks) created by nicklas
The wizard is started after successfully aligning data. In the first …
11:11 AM Ticket #629 (Use annotations on protocols in the demux and mask/align step to set ...) created by nicklas
Some program parameters for picard, bowtie, tophat, etc. are currently …
11:00 AM Changeset [2638] by nicklas
References #595: Confirm alignment Do not show the 'delete items …
9:26 AM Changeset [2637] by nicklas
References #571. Forgot to remove a few script lines.
9:24 AM Changeset [2636] by nicklas
References #571 and #547 and #548. The confirm demux wizard has been …
8:37 AM Changeset [2635] by nicklas
References #593 and #595. Changes in [2633] that ensure job folders …

Sep 3, 2014:

1:42 PM Ticket #626 (NullPointerException when registering follow-up blood) closed by nicklas
fixed: (In [2634]) Fixes #626: NullPointerException?? when registering …
1:39 PM Changeset [2634] by nicklas
Fixes #636: NullPointerException? when registering follow-up blood …
1:10 PM Changeset [2633] by nicklas
References #593 and #595. Added "delete items created by failed jobs" …
9:26 AM Ticket #628 (Add right-click menu to create pools wizard) created by nicklas
Right-clicking on a well in the lib plate should display a menu with …
9:20 AM net.sf.basedb.reggie edited by nicklas
Relesed Reggie 2.16-beta-3 (diff)
9:19 AM reggie-2.16-beta-3.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16-beta-3
9:18 AM Changeset [2632] by nicklas
Tagging Reggie 2.16-beta-3
9:17 AM Changeset [2631] by nicklas
Preparing to release Reggie 2.16-beta-3
9:02 AM Changeset [2630] by nicklas
References #593: Start masking and alignment Save aligned data from …

Sep 2, 2014:

4:08 PM Ticket #627 (Improve error visualization in wizards) closed by nicklas
fixed: (In [2629]) Fixes #627: Improve error visualization in wizards Added …
4:08 PM Changeset [2629] by nicklas
Fixes #627: Improve error visualization in wizards Added a CSS …
4:05 PM Ticket #627 (Improve error visualization in wizards) created by nicklas
Sometimes it can be a bit hard to spot the error icon next to an input …
2:12 PM Changeset [2628] by nicklas
References #547: Start Demux and Merge Display warning if the …
12:05 PM Changeset [2627] by nicklas
References #547: Start Demux and Merge Sequencing runs are sorted by …
11:43 AM Changeset [2626] by nicklas
References #547 and #593. Use the "Send message when plugin completes" …
11:39 AM Changeset [2625] by nicklas
References #593: Start masking and alignment Add -f flag to 'mv' …
11:01 AM Changeset [2624] by nicklas
References #571: Update Reggie to new scripting pattern Bad tag in …
11:01 AM Changeset [2623] by nicklas
References #571: Update Reggie to new scripting pattern Changes to …
11:00 AM Changeset [2622] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
9:17 AM Ticket #626 (NullPointerException when registering follow-up blood) created by nicklas
This seems to happing if a CASE is linked to at least two SPECIMENT or …

Sep 1, 2014:

3:52 PM Changeset [2621] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
2:55 PM Changeset [2620] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
1:57 PM Changeset [2619] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
1:45 PM Changeset [2618] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
12:43 PM Changeset [2617] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
12:42 PM Changeset [2616] by nicklas
References #571: Update Reggie to new scripting pattern Found a bug …
8:06 AM Changeset [2615] by nicklas
References #571: Update Reggie to new scripting pattern Found some …

Aug 29, 2014:

3:36 PM Ticket #625 (Prevent registration of patients with identical data) closed by nicklas
fixed: (In [2614]) Fixes #625: Prevent registration of patients with …
3:36 PM Changeset [2614] by nicklas
Fixes #625: Prevent registration of patients with identical data When …
2:15 PM Changeset [2613] by nicklas
References #625: Prevent registration of patients with identical data …
12:20 PM Ticket #625 (Prevent registration of patients with identical data) created by nicklas
The scenario is that two different users are registering patient …
11:34 AM Changeset [2612] by nicklas
References #571: Update Reggie to new scripting pattern Fixed the …
11:01 AM Changeset [2611] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …

Aug 28, 2014:

4:02 PM Changeset [2610] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
3:29 PM Changeset [2609] by nicklas
References #571: Update Reggie to new scripting pattern New file part …
3:29 PM Changeset [2608] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
8:40 AM Ticket #624 (Improve performance of the "Missing data" export wizard) closed by nicklas
fixed: (In [2607]) Fixes #624: Improve performance of the "Missing data" …
8:40 AM Changeset [2607] by nicklas
Fixes #624: Improve performance of the "Missing data" export wizard

Aug 27, 2014:

3:48 PM Ticket #624 (Improve performance of the "Missing data" export wizard) created by nicklas
Similar to #623, but a bit more complicated since it checks data at …
3:29 PM Changeset [2606] by nicklas
References #623: Improve performance of the "Missing consent" export …
3:27 PM Ticket #623 (Improve performance of the "Missing consent" export wizard) closed by nicklas
fixed: (In [2605]) Fixes #623: Improve performance of the "Missing consent" …
3:27 PM Changeset [2605] by nicklas
Fixes #623: Improve performance of the "Missing consent" export wizard
2:58 PM Ticket #623 (Improve performance of the "Missing consent" export wizard) created by nicklas
This takes a very long time. The main reason seems to be that the …
2:56 PM Changeset [2604] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
2:17 PM Changeset [2603] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
12:47 PM Changeset [2602] by nicklas
References #571: Update Reggie to new scripting pattern Updated the …
11:37 AM Ticket #622 (Updating a blood sample for a case with follow-up blood samples fails) closed by nicklas
fixed: (In [2601]) Fixes #622: Updating a blood sample for a case with …
11:37 AM Changeset [2601] by nicklas
Fixes #622: Updating a blood sample for a case with follow-up blood …
11:30 AM Ticket #622 (Updating a blood sample for a case with follow-up blood samples fails) created by nicklas
After entering the case number the wizard display the following error …
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