Timeline



Sep 19, 2019: Today

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: Yesterday

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 …

Sep 10, 2019:

1:33 PM Tickets #1159,​1157,​1172 batch updated by Nicklas Nordborg
fixed
11:05 AM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
Added more details about barcode template bioplates (diff)

Sep 6, 2019:

10:44 AM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
Added note about sequence order for the second barcode read (diff)
10:39 AM Changeset [5592] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Implemented support for …

Sep 4, 2019:

2:35 PM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
Added note about updating BASE and about the DNANormalization protocol (diff)
2:22 PM Changeset [5591] by Nicklas Nordborg
References #1129: DNA pre-normalization The DNA/RNA/Flowthrough …
9:26 AM Changeset [5590] by Nicklas Nordborg
References #1131: Switch to BASE 3.15 Switched to BASE 3.15.2 since …
9:00 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Added a row for Reggie 4.23 to the download table to make it easier to … (diff)
8:58 AM net.sf.basedb.reggie/notes423 edited by Nicklas Nordborg
More update instructions (diff)
8:09 AM Changeset [5589] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Added fqpaste.pl to the …

Aug 30, 2019:

1:51 PM Changeset [5588] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline The "read group" file …
11:31 AM Changeset [5587] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Now generates a "read …

Aug 29, 2019:

1:52 PM Changeset [5586] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Changes the MIPs demux …

Aug 26, 2019:

2:19 PM Changeset [5585] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Allow barcode names to …
2:16 PM Changeset [5584] by Nicklas Nordborg
References #1161: Update picard to 2.20 If we set the …

Aug 21, 2019:

2:44 PM Ticket #1173 (Link a single <host> entry to more than one OpenGrid cluster) closed by Nicklas Nordborg
fixed: In 5583: […]
2:44 PM Changeset [5583] by Nicklas Nordborg
Fixes #1173: Link a single <host> entry to more than one OpenGrid? cluster
1:44 PM Ticket #1173 (Link a single <host> entry to more than one OpenGrid cluster) created by Nicklas Nordborg
In reggie-config.xml a <host> entry is linked to an OpenGrid …
1:04 PM Changeset [5582] by Nicklas Nordborg
References #1146 and #1142. Changed the MIPsSecondaryAnalysis role …
9:07 AM Changeset [5581] by Nicklas Nordborg
References #1172: The message in the "Secondary analysis cleanup" …

Aug 20, 2019:

2:44 PM Ticket #1172 (The message in the "Secondary analysis cleanup" wizard is confusing) created by Nicklas Nordborg
When entering the "Secondary analysis cleanup" wizard it will make a …
9:48 AM Changeset [5580] by Nicklas Nordborg
References #1132: Implement an "Activity log" Added name of pipeline …
9:22 AM Ticket #1171 (Hisat alignment stops without error if the genotype VCF file can't be ...) closed by Nicklas Nordborg
fixed: In 5579: […]
9:22 AM Changeset [5579] by Nicklas Nordborg
Fixes #1171: Hisat alignment stops without error if the genotype VCF …
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