Timeline



May 15, 2023:

8:38 AM Changeset [7171] by Nicklas Nordborg
8:36 AM Ticket #1481 (Lab protocol for moving samples between transport and storage boxes) updated by Nicklas Nordborg
Summary changed
7:43 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7170: […]
7:43 AM Changeset [7170] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 12, 2023:

1:19 PM Changeset [7169] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.46
1:06 PM bwa-mem2_crash.zip attached to Ticket #1486 by Nicklas Nordborg
R1 and R2 with 250 read pairs that causes bwa-mem2 to fail
1:03 PM Ticket #1486 (Add an option to run the older bwa-mem instead of bwa-mem2) created by Nicklas Nordborg
There are some issues with bwa-mem2 that causes it to crash. It is …
11:32 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7168: […]
11:32 AM Changeset [7168] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:59 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7167: […]
9:59 AM Changeset [7167] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:46 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7166: […]
9:46 AM Changeset [7166] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:12 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7165: […]
9:12 AM Changeset [7165] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
8:51 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7164: […]
8:51 AM Changeset [7164] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
8:33 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7163: […]
8:33 AM Changeset [7163] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
8:29 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7162: […]
8:29 AM Changeset [7162] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 11, 2023:

2:43 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7161: […]
2:43 PM Changeset [7161] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:32 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7160: […]
9:32 AM Changeset [7160] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:01 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7159: […]
9:01 AM Changeset [7159] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 10, 2023:

1:27 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7158: […]
1:27 PM Changeset [7158] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
7:58 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7157: […]
7:58 AM Changeset [7157] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
7:46 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7156: […]
7:46 AM Changeset [7156] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
7:39 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7155: […]
7:39 AM Changeset [7155] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 9, 2023:

9:00 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7154: […]
9:00 AM Changeset [7154] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
8:56 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7153: […]
8:56 AM Changeset [7153] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
8:54 AM Ticket #1484 (Add support for searching on the ExternalRef annotation in the Case summary) updated by Nicklas Nordborg
In 7152: […]
8:54 AM Changeset [7152] by Nicklas Nordborg
References #1484: Add support for searching on the ExternalRef
8:49 AM Ticket #1485 (Add a link to view the JSON file for specimen that has been imported ...) closed by Nicklas Nordborg
fixed: In 7151: […]
8:49 AM Changeset [7151] by Nicklas Nordborg
Fixes #1485: Add a link to view the JSON file for specimen that has …
8:37 AM Ticket #1485 (Add a link to view the JSON file for specimen that has been imported ...) created by Nicklas Nordborg
8:15 AM Ticket #1484 (Add support for searching on the ExternalRef annotation in the Case summary) closed by Nicklas Nordborg
fixed: In 7150: […]
8:15 AM Changeset [7150] by Nicklas Nordborg
Fixes #1484: Add support for searching on the ExternalRef annotation …
7:35 AM Ticket #1484 (Add support for searching on the ExternalRef annotation in the Case summary) created by Nicklas Nordborg

May 8, 2023:

4:40 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7149: […]
4:40 PM Changeset [7149] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
4:40 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7148: […]
4:40 PM Changeset [7148] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
2:21 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7147: […]
2:21 PM Changeset [7147] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
2:19 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7146: […]
2:19 PM Changeset [7146] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 5, 2023:

3:04 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7145: […]
3:03 PM Changeset [7145] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
12:49 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7144: […]
12:49 PM Changeset [7144] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …
9:19 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7143: […]
9:19 AM Changeset [7143] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 4, 2023:

1:31 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7142: […]
1:31 PM Changeset [7142] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

May 2, 2023:

11:48 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7141: […]
11:48 AM Changeset [7141] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

Apr 28, 2023:

9:47 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7140: […]
9:47 AM Changeset [7140] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

Apr 27, 2023:

2:16 PM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
In 7139: […]
2:16 PM Changeset [7139] by Nicklas Nordborg
References #1480: Create import wizard for transfer of external …

Apr 26, 2023:

1:07 PM Ticket #1479 (Add support for creating storage boxes for externally process samples) updated by Nicklas Nordborg
In 7138: […]
1:07 PM Changeset [7138] by Nicklas Nordborg
References #1479: Add support for creating storage boxes for …

Apr 25, 2023:

8:49 AM Ticket #1483 (Add support for using the WGS blood items in the Genotype QC wizard) created by Nicklas Nordborg
When we have verified that genotype QC results from the WGS blood …
8:45 AM Ticket #1478 (Implement wizards for registration of samples transfered from an ...) updated by Nicklas Nordborg
Description changed
8:45 AM Ticket #1482 (Registration wizard for moving tubes between a transport box and a ...) created by Nicklas Nordborg
See also #1478 and #1481. This wizard should register the result of …
8:41 AM Ticket #1481 (Lab protocol for moving samples between transport and storage boxes) created by Nicklas Nordborg
See also #1478 and #1480. We will have item lists that represents a …
8:02 AM Ticket #1478 (Implement wizards for registration of samples transfered from an ...) updated by Nicklas Nordborg
Description changed
8:02 AM Ticket #1480 (Create import wizard for transfer of external samples) updated by Nicklas Nordborg
Description changed
8:01 AM Ticket #1480 (Create import wizard for transfer of external samples) created by Nicklas Nordborg
See also #1478. We will get information about transfered samples from …
7:48 AM Ticket #1479 (Add support for creating storage boxes for externally process samples) created by Nicklas Nordborg
See #1478. The existing storage box creation wizard should be …

Apr 24, 2023:

2:57 PM Ticket #1478 (Implement wizards for registration of samples transfered from an ...) created by Nicklas Nordborg
Material in the for of Specimen, Lysate, RNA, DNA and FlowThrough is …
12:47 PM Changeset [7137] by Nicklas Nordborg
Changes for future release Reggie 4.47
12:46 PM Milestone Reggie v4.46 completed
See Reggie extension page for more information.
12:45 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.46 (diff)
12:43 PM reggie-4.46.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.46
12:42 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) closed by Nicklas Nordborg
fixed
12:41 PM Changeset [7136] by Nicklas Nordborg
Tagging Reggie 4.46
12:41 PM Changeset [7135] by Nicklas Nordborg
Preparing to release Reggie 4.46
9:51 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7134: […]
9:51 AM Changeset [7134] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Do not …
9:37 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7133: […]
9:37 AM Changeset [7133] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
9:36 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7132: […]
9:36 AM Changeset [7132] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
9:34 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7131: […]
9:34 AM Changeset [7131] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Apr 21, 2023:

2:28 PM Changeset [7130] by Nicklas Nordborg
Changes for future release Variant Search 1.9
2:27 PM Milestone Variant Search v1.8 completed
See Variant Search extension page for …
2:26 PM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.8 (diff)
2:25 PM varsearch-1.8.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.8
2:24 PM Ticket #1467 (Switch to BASE 3.19.8 and use the new service logging implementation) closed by Nicklas Nordborg
fixed
2:23 PM Changeset [7129] by Nicklas Nordborg
Tagging Variant Search 1.8
2:22 PM Changeset [7128] by Nicklas Nordborg
Preparing to release Variant Search 1.8
1:58 PM Changeset [7127] by Nicklas Nordborg
Changes for future release Job scheduler 1.11
1:57 PM Milestone Job scheduler extension v1.10 completed
See the Job scheduler extension page for …
1:56 PM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.10 (diff)
1:53 PM opengrid-1.10.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job scheduler 1.10
1:52 PM Changeset [7126] by Nicklas Nordborg
Tagging Job scheduler 1.10
1:51 PM Changeset [7125] by Nicklas Nordborg
Preparing to release Job scheduler 1.10
12:00 PM Ticket #1466 (Switch to BASE 3.19.8 and use the new service logging implementation) updated by Nicklas Nordborg
Milestone changed
Milestone renamed
12:00 PM Tickets #1455,​1458,​1459 batch updated by Nicklas Nordborg
Milestone changed
Milestone renamed
11:57 AM Ticket #1466 (Switch to BASE 3.19.8 and use the new service logging implementation) closed by Nicklas Nordborg
fixed
11:35 AM Ticket #1476 (Implement a nice viewer for result and log files) closed by Nicklas Nordborg
fixed
11:31 AM Ticket #1472 (Use the new service logging implementation) closed by Nicklas Nordborg
fixed
11:30 AM Ticket #1470 (Use multiple threads when loading existing VCF files in the genotype ...) closed by Nicklas Nordborg
fixed
11:19 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7124: […]
11:19 AM Changeset [7124] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Fixed …
9:29 AM Ticket #1477 (The Hisat/2023 pipeline should not flag RNA items) closed by Nicklas Nordborg
fixed: In 7123: […]
9:29 AM Changeset [7123] by Nicklas Nordborg
Fixes #1477: The Hisat/2023 pipeline should not flag RNA items Also …
9:19 AM Ticket #1477 (The Hisat/2023 pipeline should not flag RNA items) updated by Nicklas Nordborg
In 7122: […]
9:19 AM Changeset [7122] by Nicklas Nordborg
References #1477: The Hisat/2023 pipeline should not flag RNA items …
9:15 AM Ticket #1475 (Validation of laterality fails with error if it is missing in the JSON ...) closed by Nicklas Nordborg
fixed: In 7121: […]
9:15 AM Changeset [7121] by Nicklas Nordborg
Fixes #1475: Validation of laterality fails with error if it is …

Apr 20, 2023:

1:29 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7120: […]
1:29 PM Changeset [7120] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
1:13 PM Ticket #1475 (Validation of laterality fails with error if it is missing in the JSON ...) updated by Nicklas Nordborg
Milestone, Summary changed
1:12 PM Ticket #1477 (The Hisat/2023 pipeline should not flag RNA items) created by Nicklas Nordborg
The auto-confirmation for the Hisat/2023 have the same rules as the …

Apr 19, 2023:

12:59 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7119: […]
12:59 PM Changeset [7119] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Apr 18, 2023:

3:37 PM Changeset [7118] by Nicklas Nordborg
Implement #1476: Implement a nice viewer for result and log files …
9:35 AM Changeset [7117] by Nicklas Nordborg
Implement #1476: Implement a nice viewer for result and log files …

Apr 17, 2023:

2:18 PM Changeset [7116] by Nicklas Nordborg
Implement #1476: Implement a nice viewer for result and log files …
2:03 PM Changeset [7115] by Nicklas Nordborg
Implement #1476: Implement a nice viewer for result and log files …
11:26 AM Ticket #1476 (Implement a nice viewer for result and log files) updated by Nicklas Nordborg
Description changed
11:24 AM Ticket #1476 (Implement a nice viewer for result and log files) created by Nicklas Nordborg
Log files and other result files from the secondary analysis often …
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