Timeline



Dec 19, 2019:

2:16 PM Changeset [5802] by Nicklas Nordborg
References #1216: Finalize the "Confirm MIPs demux" wizard Number of …
2:03 PM Ticket #1219 (Start demux wizard for MIPs should be a separate wizard) closed by Nicklas Nordborg
fixed: In 5801: […]
2:03 PM Changeset [5801] by Nicklas Nordborg
Fixes #1219: Start demux wizard for MIPs should be a separate wizard
10:56 AM Ticket #1219 (Start demux wizard for MIPs should be a separate wizard) created by Nicklas Nordborg
The "Start demux" wizard is currently shared between the RNAseq and …
10:51 AM Changeset [5800] by Nicklas Nordborg
References #1216: Finalize the "Confirm MIPs demux" wizard Metrics …

Dec 18, 2019:

1:12 PM Changeset [5799] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Added …
11:34 AM Changeset [5798] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Added …
8:33 AM Changeset [5797] by Nicklas Nordborg
References #1216: Finalize the "Confirm MIPs demux" wizard Added some …
7:32 AM Ticket #1216 (Finalize the "Confirm MIPs demux" wizard) reopened by Nicklas Nordborg
I think we should add columns with Libplate+location and Barcode …

Dec 16, 2019:

2:35 PM Changeset [5796] by Nicklas Nordborg
References #1215: Include mutation signature analysis in the variant …
2:33 PM Changeset [5795] by Nicklas Nordborg
References #1215: Include mutation signature analysis in the variant …
12:44 PM Changeset [5794] by Nicklas Nordborg
References #1215: Include mutation signature analysis in the variant …
11:30 AM Changeset [5793] by Nicklas Nordborg
References #1215: Include mutation signature analysis in the variant …
9:03 AM Changeset [5792] by Nicklas Nordborg
References #1215: Include mutation signature analysis in the variant …
8:32 AM Ticket #1217 (DoNotUse flags and comments should be copied to new child items) closed by Nicklas Nordborg
fixed: In 5791: […]
8:32 AM Changeset [5791] by Nicklas Nordborg
Fixes #1217: DoNotUse? flags and comments should be copied to new child …

Dec 13, 2019:

2:26 PM Changeset [5790] by Nicklas Nordborg
References #1217: DoNotUse? flags and comments should be copied to new …
1:58 PM Changeset [5789] by Nicklas Nordborg
References #1217: DoNotUse? flags and comments should be copied to new …
11:49 AM Ticket #1216 (Finalize the "Confirm MIPs demux" wizard) closed by Nicklas Nordborg
fixed: In 5788: […]
11:49 AM Changeset [5788] by Nicklas Nordborg
Fixes #1216: Finalize the "Confirm MIPs demux" wizard The wizard now …
11:02 AM Changeset [5787] by Nicklas Nordborg
References #1216: Finalize the "Confirm MIPs demux" wizard Added the …
9:36 AM Ticket #1218 (Implement MIPs alignment) created by Nicklas Nordborg
The next step after demux in the MIPs pipeline is an alignment step. A …
9:33 AM Ticket #1217 (DoNotUse flags and comments should be copied to new child items) created by Nicklas Nordborg
In wizards with manual selection it is possible to select items with a …
9:26 AM Ticket #1216 (Finalize the "Confirm MIPs demux" wizard) created by Nicklas Nordborg
This wizard is full with TODO that are mostly related to not knowing …
9:23 AM Ticket #1214 (Add support for external specimen) closed by Nicklas Nordborg
fixed
9:22 AM Changeset [5786] by Nicklas Nordborg
References #1214: Add support for external specimen Fixes an issue …

Dec 12, 2019:

2:26 PM Changeset [5785] by Nicklas Nordborg
References #1214: Add support for external specimen When an external …
8:30 AM Changeset [5784] by Nicklas Nordborg
References #1214: Add support for external specimen Histology images …
8:08 AM Changeset [5783] by Nicklas Nordborg
References #1214: Add support for external specimen Display "External …

Dec 11, 2019:

4:00 PM Changeset [5782] by Nicklas Nordborg
References #1214: Add support for external specimen Changes to …
1:08 PM Ticket #1215 (Include mutation signature analysis in the variant calling pipeline) created by Nicklas Nordborg
A mutation signature can be calculated from the filtered variants VCF. …
12:53 PM Ticket #1214 (Add support for external specimen) created by Nicklas Nordborg
This would be similar to the current support for external RNA items …
12:34 PM Changeset [5781] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Added support …

Dec 10, 2019:

2:29 PM Ticket #1213 (Firefox fails to open some Print dialogs) closed by Nicklas Nordborg
fixed: In 5780: […]
2:29 PM Changeset [5780] by Nicklas Nordborg
Fixes #1213: Firefox fails to open some Print dialogs The dialogs are …
2:10 PM Ticket #1213 (Firefox fails to open some Print dialogs) created by Nicklas Nordborg
There are several places in Reggie were a "Print" button should open a …
9:03 AM Changeset [5779] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Added a …

Dec 9, 2019:

9:53 AM Ticket #1212 (Enable filtering step for variant calling in auto-confirm mode) created by Nicklas Nordborg
Auto-confirmation will currently start variant calling in raw-only …
9:40 AM Ticket #1211 (Release exporter changes due to TMA specimen importer) created by Nicklas Nordborg
When the TMA importer (#1209) is implemented we should also consider …
9:37 AM Changeset [5778] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Implemented …

Dec 6, 2019:

9:50 AM Changeset [5777] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen First version …
8:08 AM Ticket #1210 (Variant calling fails if no variants are found) closed by Nicklas Nordborg
fixed
8:07 AM Changeset [5776] by Nicklas Nordborg
References #1210: Variant calling fails if no variants are found …
7:56 AM Changeset [5775] by Nicklas Nordborg
References #1210: Variant calling fails if no variants are found …

Dec 5, 2019:

2:15 PM Ticket #1210 (Variant calling fails if no variants are found) created by Nicklas Nordborg
The first vcfanno step fails with an error message: […] If there …

Dec 4, 2019:

12:59 PM Changeset [5774] by Nicklas Nordborg
References #1209: Add support for storing TMA specimen Added new …

Dec 3, 2019:

1:40 PM Changeset [5773] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
11:56 AM Changeset [5772] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
11:54 AM Changeset [5771] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
9:40 AM Changeset [5770] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
9:38 AM Changeset [5769] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …

Dec 2, 2019:

2:22 PM Changeset [5768] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
2:20 PM Changeset [5767] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
10:52 AM Changeset [5766] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …

Nov 29, 2019:

2:30 PM Changeset [5765] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
1:49 PM Changeset [5764] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
1:11 PM Changeset [5763] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
8:33 AM Ticket #1209 (Add support for storing TMA specimen) created by Nicklas Nordborg
TMA are sometimes created by external projects. We want to track some …
7:40 AM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) created by Nicklas Nordborg
The annotation/filtering step in the variant calling pipeline is using …

Nov 28, 2019:

1:52 PM Ticket #1207 (Replace the "Nothing yet" in the activity log with a quote-of-the-day) closed by Nicklas Nordborg
fixed: In 5762: […]
1:52 PM Changeset [5762] by Nicklas Nordborg
Fixes #1207: Replace the "Nothing yet" in the activity log with a …
9:06 AM Changeset [5761] by Nicklas Nordborg
References #1207: Replace the "Nothing yet" in the activity log with a …
8:53 AM Ticket #1207 (Replace the "Nothing yet" in the activity log with a quote-of-the-day) created by Nicklas Nordborg
The "Nothing yet" message in the activity log is a bit boring. We can …

Nov 26, 2019:

1:10 PM Changeset [5760] by Nicklas Nordborg
Merged Reggie 4.24.1 to the trunk.
1:06 PM Milestone Reggie v4.24.1 completed
Bug fixes and enhancements for Reggie 4.24. Revision Log: …
1:05 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.24.1 (diff)
1:05 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.24.1 (diff)
1:04 PM reggie-4.24.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.24.1
1:03 PM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) closed by Nicklas Nordborg
fixed: Closing this for now since we need to release the other bugfixes. If …
12:59 PM Changeset [5759] by Nicklas Nordborg
Tagging Reggie 4.24.1
12:57 PM Changeset [5758] by Nicklas Nordborg
Preparing to release Reggie 4.24.1
9:25 AM Changeset [5757] by Nicklas Nordborg
References #1206: The MIPs aliquot importer should handle some values …
9:02 AM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) created by Nicklas Nordborg
Some of the columns in the file used for importing MIPs aliquots …
8:53 AM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) closed by Nicklas Nordborg
fixed
7:56 AM Changeset [5756] by olle
Refs #1029. Registration of blood and FFPE blocks updated to set …

Nov 25, 2019:

9:40 AM Changeset [5755] by Nicklas Nordborg
References #1202: Add check for duplicate barcode template in the MIPs …

Nov 22, 2019:

2:04 PM Changeset [5754] by Nicklas Nordborg
References #1202: Add check for duplicate barcode template in the MIPs …
1:46 PM Ticket #1205 (Variant calling fails with "malformed BED entry") closed by Nicklas Nordborg
fixed
1:10 PM Changeset [5753] by Nicklas Nordborg
References #1205: Variant calling fails with "malformed BED entry" …
1:02 PM Changeset [5752] by Nicklas Nordborg
References #1205: Variant calling fails with "malformed BED entry" …
12:52 PM Ticket #1205 (Variant calling fails with "malformed BED entry") created by Nicklas Nordborg
The full error message: […] This seems to happen when a variant is …
11:09 AM Ticket #1204 (Change default flow cell type in MIPs create flow cells wizard) closed by Nicklas Nordborg
fixed: In 5751: […]
11:09 AM Changeset [5751] by Nicklas Nordborg
Fixes #1204: Change default flow cell type in MIPs create flow cells wizard
11:07 AM Ticket #1201 (Incorrect date is displayed for variant calling in the case summary) closed by Nicklas Nordborg
fixed: In 5750: […]
11:07 AM Changeset [5750] by Nicklas Nordborg
Fixes #1201: Incorrect date is displayed for variant calling in the …
11:02 AM Ticket #1203 (Resolve thread deadlocks) closed by Nicklas Nordborg
fixed: In 5749: […]
11:02 AM Changeset [5749] by Nicklas Nordborg
Fixes #1203: Resolve thread deadlocks This should hopefully fix the …
9:56 AM Ticket #1204 (Change default flow cell type in MIPs create flow cells wizard) created by Nicklas Nordborg
The NextSeq is the only sequencer that is used.
9:44 AM Ticket #1203 (Resolve thread deadlocks) created by Nicklas Nordborg
I have had some issues with thread deadlocks during re-installation of …

Nov 21, 2019:

1:19 PM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) created by Nicklas Nordborg
In the MIPs library registration wizard it is important that the …
1:13 PM Ticket #1201 (Incorrect date is displayed for variant calling in the case summary) created by Nicklas Nordborg
It seems like the date that is displayed is the same as the date for …
1:09 PM Changeset [5748] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.24
8:40 AM Changeset [5747] by Nicklas Nordborg
Fixes an issue with missing "N" values in the lookup tables for GC …

Nov 20, 2019:

3:03 PM Changeset [5746] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …
2:27 PM Changeset [5745] by olle
Refs #1029. Updates due to version number change to "1.6.0b7". 1. …
1:46 PM Changeset [5744] by olle
Refs #1029. Updates of BASE method calls due to update of BASE version …
8:43 AM Changeset [5743] by Nicklas Nordborg
Preparing for future release Reggie 4.25
8:41 AM Milestone Reggie v4.24 completed
See Reggie extension page for more information.
8:41 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.24 (diff)
8:40 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.24 (diff)
8:39 AM reggie-4.24.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.24
8:37 AM Changeset [5742] by Nicklas Nordborg
Tagging Reggie 4.24
8:36 AM Changeset [5741] by Nicklas Nordborg
Preparing to release Reggie 4.24
8:30 AM Changeset [5740] by Nicklas Nordborg
Merged Reggie 4.23.3 to the trunk.
8:25 AM Milestone Reggie v4.23.3 completed
Bug fixes and enhancements for Reggie 4.23.2. Revision Log: …
8:24 AM Changeset [5739] by Nicklas Nordborg
Tagging Reggie 4.23.3
8:24 AM Changeset [5738] by Nicklas Nordborg
Preparing to release Reggie 4.23.3
7:54 AM Ticket #1198 (Add support for PAD to the "Map external data" wizard) closed by Nicklas Nordborg
fixed
7:54 AM Ticket #1187 (Implement an "External RNA import" wizard) closed by Nicklas Nordborg
fixed
7:54 AM Ticket #1199 (Implement Variant calling pipeline) closed by Nicklas Nordborg
fixed
7:39 AM Changeset [5737] by Nicklas Nordborg
References #1186 and #1190. Disabling code related to the SSP plug-in …

Nov 19, 2019:

3:43 PM Changeset [5736] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Fixed some …
3:42 PM Changeset [5735] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Removed version …
11:59 AM Changeset [5734] by olle
Refs #1029. Referral form generation wizard for the NordicTrip …
11:50 AM Changeset [5733] by olle
Refs #1029. Referral form generation updated to allow projects to use …
11:23 AM Changeset [5732] by olle
Refs #1029. Referral form generation updated in generation of referral …
10:04 AM Changeset [5731] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added a variant …
Note: See TracTimeline for information about the timeline view.