Timeline



Oct 11, 2019:

1:52 PM Changeset [5663] by Nicklas Nordborg
Merge Reggie 4.23.2 to the the trunk.
1:49 PM Milestone Reggie v4.23.2 completed
Bug fixes and enhancements for Reggie 4.23.1. Revision Log: …
1:48 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.23.2 (diff)
1:48 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.23.2 (diff)
1:46 PM reggie-4.23.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.23.2
1:44 PM Changeset [5662] by Nicklas Nordborg
Tagging Reggie 4.23.2
1:44 PM Changeset [5661] by Nicklas Nordborg
Preparing to release Reggie 4.23.2
1:30 PM Ticket #1193 (The "Map external data to releases" wizard should have more options) closed by Nicklas Nordborg
fixed
1:30 PM Changeset [5660] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …
1:16 PM Ticket #1195 (The "Map external data to releases" wizard should have an option to ...) closed by Nicklas Nordborg
fixed: In 5659: […]
1:16 PM Changeset [5659] by Nicklas Nordborg
Fixes #1195: The "Map external data to releases" wizard should have an …
11:43 AM Changeset [5658] by Nicklas Nordborg
References #1195: The "Map external data to releases" wizard should …
11:04 AM Ticket #1195 (The "Map external data to releases" wizard should have an option to ...) created by Nicklas Nordborg
It would be nice if it was possible to re-order the output file based …
9:51 AM Ticket #1194 (Import more data from MIPs file) closed by Nicklas Nordborg
fixed: In 5657: […]
9:51 AM Changeset [5657] by Nicklas Nordborg
Fixes #1194: Import more data from MIPs file
9:09 AM Ticket #1194 (Import more data from MIPs file) created by Nicklas Nordborg
We should also import the PatientID and Provnummer columns. They …
9:06 AM Changeset [5656] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …
8:06 AM Changeset [5655] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …

Oct 10, 2019:

1:10 PM Changeset [5654] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …
8:43 AM Changeset [5653] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …
8:05 AM Changeset [5652] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …

Oct 9, 2019:

1:34 PM Changeset [5651] by Nicklas Nordborg
References #1193: The "Map external data to releases" wizard should …
8:49 AM Ticket #1193 (The "Map external data to releases" wizard should have more options) created by Nicklas Nordborg
The wizard currently expects that the first column contains personal …
8:36 AM Changeset [5650] by Nicklas Nordborg
References #1190: SCAN-B report Linked a report template to a …
7:39 AM Ticket #1191 (Remove debug output from GenotypeMessage) closed by Nicklas Nordborg
fixed: In 5649: […]
7:39 AM Changeset [5649] by Nicklas Nordborg
Fixes #1191: Remove debug output from GenotypeMessage?

Oct 8, 2019:

3:51 PM Ticket #1192 (The "Flag RNA" option should not be checked by default in legacy ...) closed by Nicklas Nordborg
fixed: In 5648: […]
3:51 PM Changeset [5648] by Nicklas Nordborg
Fixes #1192: The "Flag RNA" option should not be checked by default in …
2:05 PM Ticket #1192 (The "Flag RNA" option should not be checked by default in legacy ...) created by Nicklas Nordborg
Jobs that fail due to some unexpected crash should not cause the "Flag …
1:39 PM Changeset [5647] by Nicklas Nordborg
References #1190: SCAN-B report Added first version of a SCAN-B …
9:36 AM Ticket #1191 (Remove debug output from GenotypeMessage) created by Nicklas Nordborg
The call to System.out.println() at …
8:03 AM Ticket #1190 (SCAN-B report) created by Nicklas Nordborg
A new report, the "SCAN-B report" should be implemented. It will …

Oct 7, 2019:

2:18 PM Ticket #1188 (Register destruction of stored samples and extracts in the "Retraction ...) closed by Nicklas Nordborg
fixed
1:31 PM Changeset [5646] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
11:20 AM Ticket #1189 (The retraction destruction wizard try to connect to the file server ...) closed by Nicklas Nordborg
fixed: In 5645: […]
11:20 AM Changeset [5645] by Nicklas Nordborg
Fixes #1189: The retraction destruction wizard try to connect to the …
11:07 AM Ticket #1189 (The retraction destruction wizard try to connect to the file server ...) created by Nicklas Nordborg
When running the retraction wizard for final deletion of items there …
9:57 AM Changeset [5644] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
9:36 AM Changeset [5643] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …

Oct 4, 2019:

9:39 AM Changeset [5642] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
8:20 AM Changeset [5641] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
8:19 AM Changeset [5640] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …

Oct 3, 2019:

3:10 PM Changeset [5639] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
9:47 AM Changeset [5638] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …
8:25 AM Changeset [5637] by Nicklas Nordborg
References #1188: Register destruction of stored samples and extracts …

Oct 2, 2019:

1:30 PM Ticket #1188 (Register destruction of stored samples and extracts in the "Retraction ...) created by Nicklas Nordborg
The typical situation is that a "Retract" or "RetroNo?" is received and …
1:07 PM Changeset [5636] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Added …

Oct 1, 2019:

3:42 PM Changeset [5635] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Display …
3:09 PM Changeset [5634] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Added …

Sep 30, 2019:

2:11 PM Changeset [5633] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard …
10:56 AM Changeset [5632] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Added …

Sep 27, 2019:

1:33 PM Changeset [5631] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Added …
11:12 AM Changeset [5630] by Nicklas Nordborg
References #1187: Implement an "External RNA import" wizard Added …

Sep 26, 2019:

1:49 PM Changeset [5629] by Nicklas Nordborg
Found a debug message that should not be there.
7:51 AM Ticket #1119 (Re-implement TIFF to JPG conversion for Histology images using the ...) closed by Nicklas Nordborg
fixed: This ticket had already been fixed.

Sep 25, 2019:

8:46 AM Ticket #1187 (Implement an "External RNA import" wizard) created by Nicklas Nordborg
Should be similar to the MIPs DNA importer, but a lot simpler. We need …

Sep 24, 2019:

3:52 PM Changeset [5628] by Nicklas Nordborg
References #1186: Implement plug-in for running Single Sample …
2:43 PM Changeset [5627] by Nicklas Nordborg
References #1186: Implement plug-in for running Single Sample …
2:22 PM Changeset [5626] by Nicklas Nordborg
References #1186: Implement plug-in for running Single Sample …
1:21 PM Ticket #1186 (Implement plug-in for running Single Sample Predictor models) created by Nicklas Nordborg
To start testing the Single Sample Predictor integration with BASE a …

Sep 23, 2019:

2:31 PM net.sf.basedb.reggie/HistoryOfReggie edited by Nicklas Nordborg
Added Reggie 4.23.1 (diff)
2:30 PM reggie-4.23.1.png attached to net.sf.basedb.reggie/HistoryOfReggie by Nicklas Nordborg
Reggie 4.23.1
1:32 PM Milestone Reggie v4.23.1 completed
Bug fixes and enhancements for Reggie 4.23. Revision Log: …
1:31 PM Changeset [5625] by Nicklas Nordborg
Changes for future release Reggie 4.24
1:30 PM Changeset [5624] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.23
1:28 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.23.1 (diff)
1:28 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.23.1 (diff)
1:27 PM reggie-4.23.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.23.1
1:25 PM Changeset [5623] by Nicklas Nordborg
Tagging Reggie 4.23.1
1:24 PM Changeset [5622] by Nicklas Nordborg
Preparing to release Reggie 4.23.1
1:17 PM Ticket #1178 (Scripts should not fail if it can't change group on files) closed by Nicklas Nordborg
fixed: Since there is no good way to report back warnings from the other …
8:26 AM Changeset [5621] by Nicklas Nordborg
References #1181: Incorrect counter for pilot reports in the activity …

Sep 20, 2019:

1:40 PM Ticket #1185 (Add link to the demultiplex metrics file in the "Confirm demux" wizards) closed by Nicklas Nordborg
fixed: In 5620: […]
1:40 PM Changeset [5620] by Nicklas Nordborg
Fixes #1185: Add link to the demultiplex metrics file in the "Confirm …
11:56 AM Ticket #1185 (Add link to the demultiplex metrics file in the "Confirm demux" wizards) created by Nicklas Nordborg
It would be nice if this file could easily be accessed instead of …
11:30 AM Changeset [5619] by Nicklas Nordborg
References #1178: Scripts should not fail if it can't change group on …
8:51 AM Changeset [5618] by Nicklas Nordborg
References #1178: Scripts should not fail if it can't change group on …
8:43 AM Ticket #1184 (Increase the number of entries displayed by the activity log) closed by Nicklas Nordborg
fixed: In 5617: […]
8:43 AM Changeset [5617] by Nicklas Nordborg
Fixes #1184: Increase the number of entries displayed by the activity …

Sep 19, 2019:

2:50 PM Ticket #1184 (Increase the number of entries displayed by the activity log) created by Nicklas Nordborg
This seems to currently be limited to 25, but there is room for more. …
1:13 PM Ticket #1183 (Change to picard 2.20.8 or later) closed by Nicklas Nordborg
fixed: In 5616: […]
1:13 PM Changeset [5616] by Nicklas Nordborg
Fixes #1183: Change to picard 2.20.8 or later
1:10 PM Ticket #1183 (Change to picard 2.20.8 or later) created by Nicklas Nordborg
This version includes an improvement in ExtractIlluminaBarcodes that …
9:46 AM Ticket #1182 (Activity log entry for "pilot reports" should be registered by ...) closed by Nicklas Nordborg
fixed: In 5615: […]
9:46 AM Changeset [5615] by Nicklas Nordborg
Fixes #1182: Activity log entry for "pilot reports" should be …
8:50 AM Ticket #1182 (Activity log entry for "pilot reports" should be registered by ...) created by Nicklas Nordborg
Right now it is logged as if the report was manually created.
8:33 AM Ticket #1181 (Incorrect counter for pilot reports in the activity log) closed by Nicklas Nordborg
fixed: In 5614: […]
8:33 AM Changeset [5614] by Nicklas Nordborg
Fixes #1181: Incorrect counter for pilot reports in the activity log …
8:12 AM Ticket #1181 (Incorrect counter for pilot reports in the activity log) created by Nicklas Nordborg
Created 16777214 pilot reports This is clearly not correct. The …

Sep 18, 2019:

2:14 PM Ticket #1179 (The "Number of slots" value in the Start demux wizard is always from ...) closed by Nicklas Nordborg
fixed: In 5613: […]
2:14 PM Changeset [5613] by Nicklas Nordborg
Fixes #1179: The "Number of slots" value in the Start demux wizard is …
1:11 PM Ticket #1180 (Activity log entry for "sequencing ended" should be registered by ...) closed by Nicklas Nordborg
fixed: In 5612: […]
1:11 PM Changeset [5612] by Nicklas Nordborg
Fixes #1180: Activity log entry for "sequencing ended" should be …
1:08 PM Ticket #1180 (Activity log entry for "sequencing ended" should be registered by ...) created by Nicklas Nordborg
Right now it is logged as if the sequencing was manually registered.
10:38 AM Ticket #1179 (The "Number of slots" value in the Start demux wizard is always from ...) created by Nicklas Nordborg
reggie-config.xml has a configuration option for the number of slots …
10:19 AM Ticket #1177 (Remove <add-read-groups-options> from reggie-config.xml) closed by Nicklas Nordborg
fixed: In 5611: […]
10:19 AM Changeset [5611] by Nicklas Nordborg
Fixes #1177: Remove <add-read-groups-options> from reggie-config.xml …

Sep 17, 2019:

4:53 PM Changeset [5610] by Jari Häkkinen
removed obsolete script
1:55 PM Ticket #1178 (Scripts should not fail if it can't change group on files) created by Nicklas Nordborg
See #1174. This implemented a 'chgrp' command to allow external data …

Sep 16, 2019:

2:53 PM Ticket #1177 (Remove <add-read-groups-options> from reggie-config.xml) created by Nicklas Nordborg
This configuration option is not needed since the …
9:10 AM Changeset [5609] by Nicklas Nordborg
Changes for future release Reggie 4.24
9:09 AM Milestone Reggie v4.23 completed
See Reggie extension page for more information.
9:09 AM Ticket #1146 (Demux for the MIPs pipeline) closed by Nicklas Nordborg
fixed
9:08 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.23 (diff)
9:07 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.23 (diff)
9:06 AM reggie-4.23.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.23
9:03 AM Changeset [5608] by Nicklas Nordborg
Tagging Reggie 4.23
9:03 AM Changeset [5607] by Nicklas Nordborg
Preparing to release Reggie 4.23

Sep 13, 2019:

3:03 PM Changeset [5606] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Changed default 'smp' …
1:11 PM Ticket #1176 (The keep-session-alive functionality should not hide current messages) closed by Nicklas Nordborg
fixed: In 5605: […]
1:11 PM Changeset [5605] by Nicklas Nordborg
Fixes #1176: The keep-session-alive functionality should not hide …
9:53 AM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
Renamed MIPS_Pool to MIPS_Panel (diff)
9:51 AM Ticket #1176 (The keep-session-alive functionality should not hide current messages) created by Nicklas Nordborg
I noted a problem with the MIPs plate/aliquot importer. If there are …
9:39 AM Changeset [5604] by Nicklas Nordborg
References #1136: MIPs plate lab protocol Changes related to the …
9:27 AM Changeset [5603] by Nicklas Nordborg
References #1135: Design MIPs plate wizard Changes related to the …
9:12 AM Changeset [5602] by Nicklas Nordborg
References #1129: DNA pre-normalization Changes related to the …
8:58 AM Changeset [5601] by Nicklas Nordborg
References #1130: Import wizard for MIPs aliquot plates Changed the …
8:52 AM Changeset [5600] by Nicklas Nordborg
References #1130: Import wizard for MIPs aliquot plates Changed the …
8:49 AM Changeset [5599] by Nicklas Nordborg
References #1130: Import wizard for MIPs aliquot plates Changed …

Sep 11, 2019:

3:07 PM Changeset [5598] by Nicklas Nordborg
Removing unused import.
2:29 PM Ticket #1175 (Temporary R working files may be left in open state) closed by Nicklas Nordborg
fixed: In 5597: […]
2:29 PM Changeset [5597] by Nicklas Nordborg
Fixes #1175: Temporary R working files may be left in open state
2:26 PM Ticket #1175 (Temporary R working files may be left in open state) created by Nicklas Nordborg
Assuming that the closeIn parameter is true and overwrite is …
2:14 PM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
Added information about giving read access to data files for external … (diff)
2:07 PM Ticket #1174 (Permission on files created by secondary analysis for external samples) closed by Nicklas Nordborg
fixed
1:49 PM Changeset [5596] by Nicklas Nordborg
References #1174: Permission on files created by secondary analysis …
1:32 PM Changeset [5595] by Nicklas Nordborg
References #1174: Permission on files created by secondary analysis …
12:52 PM Changeset [5594] by Nicklas Nordborg
References #1174: Permission on files created by secondary analysis …
11:14 AM Changeset [5593] by Nicklas Nordborg
References #1174: Permission on files created by secondary analysis …
9:31 AM Ticket #1174 (Permission on files created by secondary analysis for external samples) created by Nicklas Nordborg
Files that are created as part of secondary analysis are usually …
Note: See TracTimeline for information about the timeline view.