Timeline



Oct 3, 2014:

1:53 PM Changeset [2727] by Nicklas Nordborg
References #593: Start masking and alignment Switches to hg38 in the …
1:52 PM Changeset [2726] by Nicklas Nordborg
References #630: Start Cufflinks Switches to hg38 in the default …
7:48 AM Changeset [2725] by Nicklas Nordborg
References #641: Import data from cufflinks result files Schedules a …

Oct 2, 2014:

2:22 PM Changeset [2724] by Nicklas Nordborg
References #641: Import data from cufflinks result files Install …
2:18 PM Changeset [2723] by Nicklas Nordborg
References #641: Import data from cufflinks result files Change BASE …
9:09 AM Changeset [2722] by Nicklas Nordborg
References #630: Start cufflinks Added possibility to select an array …

Oct 1, 2014:

4:11 PM Changeset [2721] by Nicklas Nordborg
References #630: Start cufflinks It is possible to start and run …
4:08 PM Ticket #642 (Confirm feature extraction as completed) created by Nicklas Nordborg
This wizard should be done after running cufflinks (#630) and …
4:03 PM Ticket #641 (Import data from cufflinks result files) created by Nicklas Nordborg
When Cufflinks has completed it has created isoforms.fpkm_tracking
3:56 PM Ticket #640 (Finalize update to new scripting pattern) created by Nicklas Nordborg
Finish what was started in #571.
3:53 PM Milestone Reggie v2.15.4 completed
Bug fixes for Reggie 2.15. See [wiki:net.sf.basedb.reggie Reggie …
2:08 PM Changeset [2720] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
2:06 PM Changeset [2719] by Nicklas Nordborg
References #637: Add annotations for lot numbers in the …
2:03 PM Changeset [2718] by Nicklas Nordborg
References #637: Add annotations for lot numbers in the …
1:17 PM Changeset [2717] by Nicklas Nordborg
References #637: Add annotations for lot numbers in the …
8:53 AM Changeset [2716] by Nicklas Nordborg
References #632: Increase max volume limit in pooling wizard to 20µl …

Sep 30, 2014:

2:53 PM Changeset [2715] by Nicklas Nordborg
References #533: Add secondary analysis section to Reggie …
1:07 PM Changeset [2714] by Nicklas Nordborg
Update classpath in Eclipse.
1:04 PM Changeset [2713] by Nicklas Nordborg
Deleting obsolete branch.
1:04 PM Changeset [2712] by Nicklas Nordborg
Deleting obsolete branch.
1:03 PM Changeset [2711] by Nicklas Nordborg
Switching trunk to Reggie 2.17-dev
1:01 PM Changeset [2710] by Nicklas Nordborg
Creating 2.16-stable branch since it should be close to final release …
12:37 PM Changeset [2709] by Nicklas Nordborg
References #533: Add secondary analysis section to Reggie Making …

Sep 29, 2014:

2:35 PM Changeset [2708] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
1:51 PM Ticket #639 (Case summary may throw ItemNotFoundException) closed by Nicklas Nordborg
fixed: (In [2707]) Fixes #639: Case summary may throw ItemNotFoundException?
1:51 PM Changeset [2707] by Nicklas Nordborg
Fixes #639: Case summary may throw ItemNotFoundException?
1:47 PM Ticket #639 (Case summary may throw ItemNotFoundException) created by Nicklas Nordborg
This is an intermittent error that can only happen soon after after …
1:29 PM Changeset [2706] by Nicklas Nordborg
References #593 and #595. Parse 'accepted_hits_picardmetrics.csv' and …
1:24 PM Changeset [2705] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
8:22 AM Changeset [2704] by Nicklas Nordborg
References #533: Add secondary analysis section to Reggie Failure to …

Sep 26, 2014:

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

Sep 25, 2014:

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

Sep 24, 2014:

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

Sep 23, 2014:

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

Sep 22, 2014:

9:02 AM Changeset [2687] by Nicklas Nordborg
References #637: Add annotations for lot numbers in the …
8:30 AM Changeset [2686] by Nicklas Nordborg
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 Nordborg
For testing and evaluation purposes it is sometimes desirable to …
7:58 AM Changeset [2685] by Nicklas Nordborg
References #595: Confirm alignment Same change as [2683] for the …

Sep 18, 2014:

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

Sep 17, 2014:

4:09 PM Changeset [2677] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
10:49 AM Changeset [2676] by Nicklas Nordborg
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 Nordborg
We would like to keep track of the lot numbers for some reagents used …
9:47 AM Changeset [2675] by Nicklas Nordborg
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 Nordborg
fixed: (In [2674]) Fixes #636: INCA export may fail if there are blood …
2:28 PM Changeset [2674] by Nicklas Nordborg
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 Nordborg
The INCA export fail in this scenario: * "all" option is selected * …
8:48 AM Changeset [2673] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
7:52 AM Changeset [2672] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
7:49 AM Changeset [2671] by Nicklas Nordborg
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 Nordborg
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 Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
3:47 PM Changeset [2669] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
2:47 PM Changeset [2668] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
1:10 PM Changeset [2667] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
12:48 PM Changeset [2666] by Nicklas Nordborg
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 Nordborg
Fixed incorrect message.
8:23 AM Changeset [2664] by Nicklas Nordborg
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 Nordborg
fixed
2:35 PM Changeset [2663] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
2:14 PM Changeset [2662] by Nicklas Nordborg
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 Nordborg
fixed: (In [2661]) Fixes #633: Adapter peak fraction=0 is displayed as …
12:36 PM Changeset [2661] by Nicklas Nordborg
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 Nordborg
fixed: (In [2660]) Fixes #632: Increase max volume limit in pooling wizard to 20µl
12:29 PM Changeset [2660] by Nicklas Nordborg
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 Nordborg
12:24 PM Ticket #632 (Increase max volume limit in pooling wizard to 20µl) created by Nicklas Nordborg
10:33 AM Changeset [2659] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
9:59 AM net.sf.basedb.labenv edited by Jari Häkkinen
(diff)
9:05 AM Changeset [2658] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …

Sep 11, 2014:

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

Sep 10, 2014:

2:07 PM Changeset [2651] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
1:57 PM Changeset [2650] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
12:33 PM Changeset [2649] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
9:58 AM Changeset [2648] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
8:58 AM Changeset [2647] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
8:55 AM Changeset [2646] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern (first step) …
8:18 AM Changeset [2645] by Nicklas Nordborg
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 Nordborg
The yubikey-extended-properties.xml is part of the release since … (diff)
1:43 PM Changeset [2644] by Nicklas Nordborg
References #595: Confirm alignment The 'View remote files' dialog now …
1:33 PM Changeset [2643] by Nicklas Nordborg
References #631: Add data check to the confirm sequencing ended wizard …
1:28 PM Changeset [2642] by Nicklas Nordborg
References #631: Add data check to the confirm sequencing ended wizard …
11:38 AM Changeset [2641] by Nicklas Nordborg
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 Nordborg
Picard has a tool called CheckIlluminaDirectory which can be used …

Sep 8, 2014:

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

Sep 4, 2014:

11:14 AM Ticket #630 (Start cufflinks) created by Nicklas Nordborg
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 Nordborg
Some program parameters for picard, bowtie, tophat, etc. are currently …
11:00 AM Changeset [2638] by Nicklas Nordborg
References #595: Confirm alignment Do not show the 'delete items …
9:26 AM Changeset [2637] by Nicklas Nordborg
References #571. Forgot to remove a few script lines.
9:24 AM Changeset [2636] by Nicklas Nordborg
References #571 and #547 and #548. The confirm demux wizard has been …
8:37 AM Changeset [2635] by Nicklas Nordborg
References #593 and #595. Changes in [2633] that ensure job folders …
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