Timeline


and

Oct 13, 2014:

2:52 PM Changeset [2802] by nicklas
References #656: FASTQ files are not always stored in the expected …
2:49 PM Changeset [2801] by nicklas
Merge Reggie 2.16.1 to the trunk.
2:39 PM Changeset [2800] by nicklas
Preparing for future release Reggie 2.16.2
2:39 PM PluginDownload edited by nicklas
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 nicklas
Released Reggie 2.16.1 (diff)
2:34 PM reggie-2.16.1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16.1
2:33 PM Changeset [2799] by nicklas
Tagging Reggie 2.16.1
2:32 PM Changeset [2798] by nicklas
Preparing to release Reggie 2.16.1
2:30 PM Ticket #660 (Error in sample source report wizard) closed by nicklas
fixed: (In [2797]) Fixes #660: Error in sample source report wizard
2:30 PM Changeset [2797] by nicklas
Fixes #660: Error in sample source report wizard
2:26 PM Ticket #660 (Error in sample source report wizard) created by nicklas
Go to the sample source report wizard. Select the 'Overview report' …
1:32 PM Changeset [2796] by nicklas
References #640: Finalize update to new scripting pattern Found some …
1:31 PM Changeset [2795] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:32 AM Changeset [2794] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
9:38 AM Changeset [2793] by nicklas
Synchronize changes from #653, #654, #658 and #659 to the trunk.
9:27 AM Changeset [2792] by nicklas
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 nicklas
fixed: (In [2791]) Fixes #659: Do not trust fragement size calculated by …
9:18 AM Changeset [2791] by nicklas
Fixes #659: Do not trust fragement size calculated by bowtie if number …
9:14 AM Changeset [2790] by nicklas
References #657: Include Reggie version number in wizards Change …
9:12 AM Changeset [2789] by nicklas
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 nicklas
The FragmentSizeAvg and FragmentSizeStd should be set to -1 if the …
8:51 AM Ticket #658 (Adjust fragment size mean and standard deviation) closed by nicklas
fixed: (In [2788]) Fixes #658: Adjust fragment size mean and standard …
8:51 AM Changeset [2788] by nicklas
Fixes #658: Adjust fragment size mean and standard deviation Added …
8:41 AM Changeset [2787] by nicklas
References #653: Use explicit paths to all important program used in …
7:42 AM Changeset [2786] by nicklas
References #653: Use explicit paths to all important program used in …

Oct 10, 2014:

2:23 PM Ticket #658 (Adjust fragment size mean and standard deviation) created by nicklas
In the demux step we introduced a call to bowtie that is used to …
12:59 PM Changeset [2785] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:55 AM Changeset [2784] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:14 AM Changeset [2783] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
10:59 AM Changeset [2782] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
9:17 AM Changeset [2781] by nicklas
Tag mismatch.
9:14 AM Ticket #657 (Include Reggie version number in wizards) closed by nicklas
fixed: (In [2780]) Fixes #657: Include Reggie version number in wizards …
9:14 AM Changeset [2780] by nicklas
Fixes #657: Include Reggie version number in wizards build.xml …
9:11 AM Ticket #657 (Include Reggie version number in wizards) created by nicklas
8:27 AM Ticket #656 (FASTQ files are not always stored in the expected folder) closed by nicklas
fixed: (In [2779]) Fixes #656: FASTQ files are not always stored in the …
8:27 AM Changeset [2779] by nicklas
Fixes #656: FASTQ files are not always stored in the expected folder …

Oct 9, 2014:

12:42 PM Changeset [2778] by olle
12:41 PM Changeset [2777] by olle
12:41 PM Changeset [2776] by olle
12:32 PM Changeset [2775] by olle
Registration extension for Melanoma/Lung? cancer project.
11:39 AM Changeset [2774] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
8:40 AM Changeset [2773] by nicklas
References #656: FASTQ files are not always stored in the expected …
8:13 AM Ticket #654 (Synchronize default options for pipeline analysis) closed by nicklas
fixed
8:13 AM Changeset [2772] by nicklas
References #654: Synchronize default options for pipeline analysis …
8:10 AM Changeset [2771] by nicklas
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 nicklas
fixed: (In [2770]) Fixes #655: PT_READS is not reported correctly in …
8:09 AM Changeset [2770] by nicklas
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 nicklas
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 nicklas
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 nicklas
fixed: (In [2769]) Fixes #653: Use explicit paths to all important program …
12:51 PM Changeset [2769] by nicklas
Fixes #653: Use explicit paths to all important program used in …
11:59 AM Changeset [2768] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:52 AM Changeset [2767] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:49 AM Changeset [2766] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:48 AM Changeset [2765] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:45 AM Changeset [2764] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:43 AM Changeset [2763] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:42 AM Ticket #654 (Synchronize default options for pipeline analysis) created by nicklas
The reggie-ogs-hosts.xml file contain a lot of options for the …
11:40 AM Changeset [2762] by nicklas
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 nicklas
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 nicklas
fixed: I guess that should be most of the BASE3-compatible plug-ins/extensions.
9:37 AM Changeset [2761] by nicklas
References #652: New location of BASE JAR files YubiKey? trunk.
9:35 AM Changeset [2760] by nicklas
References #652: New location of BASE JAR files X-files trunk.
9:34 AM Changeset [2759] by nicklas
References #652: New location of BASE JAR files Normalizers trunk.
9:33 AM Changeset [2758] by nicklas
References #652: New location of BASE JAR files MeV trunk.
9:32 AM Changeset [2757] by nicklas
References #652: New location of BASE JAR files LabEnv? trunk.
9:31 AM Changeset [2756] by nicklas
References #652: New location of BASE JAR files Illumina plug-ins trunk.
9:29 AM Changeset [2755] by nicklas
References #652: New location of BASE JAR files HDFS trunk.
9:27 AM Changeset [2754] by nicklas
References #652: New location of BASE JAR files Code examples trunk.
9:26 AM Changeset [2753] by nicklas
References #652: New location of BASE JAR files FTP Server trunk.
9:24 AM Changeset [2752] by nicklas
References #652: New location of BASE JAR files Reggie trunk. But …
9:23 AM Changeset [2751] by nicklas
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 nicklas
This affects all plug-ins that has implemented automatic download of …
9:12 AM Changeset [2750] by nicklas
References #630: Start cufflinks Added support for re-mapping some …
9:06 AM Changeset [2749] by nicklas
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 nicklas
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 nicklas
Taken between the first core biopsy and the operator. Referral form …
8:17 AM Ticket #649 (Better balance in progress when demuxing) closed by nicklas
fixed: (In [2748]) Fixes #649: Better balance in progress when demuxing
8:17 AM Changeset [2748] by nicklas
Fixes #649: Better balance in progress when demuxing
8:14 AM Ticket #649 (Better balance in progress when demuxing) created by nicklas
The current implementation assigns 50% of the progress to the demux …

Oct 7, 2014:

2:45 PM Changeset [2747] by nicklas
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 nicklas
fixed: (In [2746]) Fixes #646: New options for specimen type in specimen tube …
12:36 PM Changeset [2746] by nicklas
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 nicklas
12:32 PM Changeset [2745] by nicklas
References #640: Finalize update to new scripting pattern More …

Oct 6, 2014:

3:56 PM Ticket #647 (Select specimen type per tube in specimen tube registration) closed by nicklas
fixed: (In [2744]) Fixes #647: Select specimen type per tube in specimen tube …
3:56 PM Changeset [2744] by nicklas
Fixes #647: Select specimen type per tube in specimen tube registration
3:46 PM Ticket #648 (More help texts in the specimen tube registration wizard) closed by nicklas
fixed: (In [2743]) Fixes #648: More help texts in the specimen tube …
3:46 PM Changeset [2743] by nicklas
Fixes #648: More help texts in the specimen tube registration wizard
3:41 PM Ticket #646 (New options for specimen type in specimen tube registration) closed by nicklas
fixed: (In [2742]) Fixes #646: New option for specimen type in specimen tube …
3:41 PM Changeset [2742] by nicklas
Fixes #646: New option for specimen type in specimen tube registration
3:34 PM Ticket #648 (More help texts in the specimen tube registration wizard) created by nicklas
Add some help text for 'Other path note' and 'Operator delivery …
3:32 PM Ticket #647 (Select specimen type per tube in specimen tube registration) created by nicklas
In the current implementation, the specimen type is selected in the …
3:29 PM Ticket #646 (New options for specimen type in specimen tube registration) created by nicklas
Uncertain and Normal Installation wizard needs to be updated and the …
3:03 PM Ticket #645 (More than one parent item was found when starting align job) closed by nicklas
fixed: (In [2741]) Fixes #645: More than one parent item was found when …
3:03 PM Changeset [2741] by nicklas
Fixes #645: More than one parent item was found when starting align job
2:47 PM Ticket #645 (More than one parent item was found when starting align job) created by nicklas
When starting an align job for a library that has been merged from 2 …
2:31 PM Changeset [2740] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
12:01 PM Changeset [2739] by nicklas
References #630. Check that values from the database such as paths and …
11:46 AM Ticket #644 (Can't start align job) closed by nicklas
fixed: (In [2738]) Fixes #644: Can't start align job
11:46 AM Changeset [2738] by nicklas
Fixes #644: Can't start align job
11:28 AM Ticket #644 (Can't start align job) created by nicklas
When submitting the job an error message is returned: […] I guess …
11:13 AM Ticket #643 (Pathology referral form registration doesn't validate RNA later time) closed by nicklas
fixed: (In [2737]) Fixes #643: Pathology referral form registration doesn't …
11:13 AM Changeset [2737] by nicklas
Fixes #643: Pathology referral form registration doesn't validate RNA …
11:10 AM Ticket #643 (Pathology referral form registration doesn't validate RNA later time) created by nicklas
Entering a date but no time for RNA later doesn't perform correct …
10:48 AM Changeset [2736] by nicklas
Merge Reggie 2.16 (final) to trunk.
10:02 AM Changeset [2735] by nicklas
Preparing for future release Reggie 2.16.1
9:58 AM Milestone Reggie v2.16 completed
Focus on adding support for "Secondary analysis" to Reggie. This means …
9:58 AM Ticket #530 (Display logs from temperature and humidity measurements) closed by nicklas
fixed
9:57 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16 (final) (diff)
9:56 AM reggie-2.16.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16
9:53 AM Changeset [2734] by nicklas
Tagging Reggie 2.16
9:52 AM Changeset [2733] by nicklas
Preparing to release Reggie 2.16 final.
9:49 AM Changeset [2732] by nicklas
Remove unused import.
9:48 AM Changeset [2731] by nicklas
Remove unused import.
9:48 AM Changeset [2730] by nicklas
References #547: Start Demux and Merge Add 'rm' commands in the …
8:26 AM Changeset [2729] by nicklas
References #547, #593 and #631. Check that values from the database …
7:52 AM Changeset [2728] by nicklas
References #548: Register Demux and Merge as ended Display '-' …

Oct 3, 2014:

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

Oct 2, 2014:

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

Oct 1, 2014:

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

Sep 30, 2014:

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

Sep 29, 2014:

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

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) …
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