Timeline



Jul 5, 2019:

1:36 PM Changeset [5541] by olle
Refs #1029. FFPE block registration updated in step 3 with support for …

Jul 4, 2019:

1:51 PM Changeset [5540] by olle
Refs #1029. Updates due to update of Java version from to 1.8 to …

Jun 28, 2019:

2:35 PM Ticket #1160 (Investigate changes in Picard since our last modified version) closed by Nicklas Nordborg
fixed
2:35 PM Ticket #1161 (Update picard to 2.20) closed by Nicklas Nordborg
fixed
2:33 PM Changeset [5539] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Added support for …
2:28 PM Changeset [5538] by Nicklas Nordborg
References #1146: Demux for the MIPs pipeline Demux parameters has …
10:51 AM Changeset [5537] by Nicklas Nordborg
References #1161: Update picard to 2.20 Updated MarkDuplicates step …
8:47 AM Changeset [5536] by Nicklas Nordborg
References #1161: Update picard to 2.20 Updated the RNA-seq demux to …

Jun 27, 2019:

2:15 PM Changeset [5535] by Nicklas Nordborg
References #1161: Update picard to 2.20 Removed all …
2:00 PM Changeset [5534] by Nicklas Nordborg
References #1161 and #1146. The MIPs demux is now running with picard …
12:43 PM Ticket #1163 (Start demux wizard may display the same sequencing run multiple times ...) closed by Nicklas Nordborg
fixed: In 5533: […]
12:43 PM Changeset [5533] by Nicklas Nordborg
Fixes #1163: Start demux wizard may display the same sequencing run …
12:41 PM Ticket #1163 (Start demux wizard may display the same sequencing run multiple times ...) created by Nicklas Nordborg
This seems to happen if a sequencing run has already been demuxed more …
11:24 AM Changeset [5532] by Nicklas Nordborg
References #1162: Add support for using 'M' in the read-string when …
11:00 AM Changeset [5531] by Nicklas Nordborg
References #1161: Update picard to 2.20 Implemented a method for …
9:43 AM Changeset [5530] by Nicklas Nordborg
References #1162: Add support for using 'M' in the read-string when …
9:34 AM Changeset [5529] by Nicklas Nordborg
References #1161: Update picard to 2.20 Adding the picard2 wrapper …
9:33 AM Changeset [5528] by Nicklas Nordborg
References #1161: Update picard to 2.20 Updated to the new command …
9:08 AM Changeset [5527] by Nicklas Nordborg
References #1161: Update picard to 2.20 Changed the default …
7:49 AM Ticket #1162 (Add support for using 'M' in the read-string when demuxing) created by Nicklas Nordborg
This is needed to handle UMI:s in the MIPs pipeline. It requires the …
7:45 AM Ticket #1161 (Update picard to 2.20) created by Nicklas Nordborg
http://broadinstitute.github.io/picard/ I think we should manage …

Jun 26, 2019:

9:29 AM Ticket #1160 (Investigate changes in Picard since our last modified version) created by Nicklas Nordborg
We are using a modified version of Picard for demuxing. It is base on …

Jun 25, 2019:

9:39 AM Ticket #1159 (Release exporter changes due to MIPs pipeline) created by Nicklas Nordborg
The first task is to make sure that existing items in the RNA-seq …
9:28 AM Tickets #1130,​1135,​1136,​1137,​1138,​1142 batch updated by Nicklas Nordborg
fixed
9:25 AM Ticket #1145 (Location of data for external RNA) closed by Nicklas Nordborg
fixed
9:25 AM Ticket #1129 (DNA pre-normalization) closed by Nicklas Nordborg
fixed
9:24 AM Ticket #1133 (Re-organize the Reggie front page) closed by Nicklas Nordborg
fixed
9:05 AM Changeset [5526] by Nicklas Nordborg
References #1130, #1135, #1142, #1146. Fixing and getting rid of some …
7:54 AM Changeset [5525] by Nicklas Nordborg
References #1154: Switch to Java 11 and BASE 3.15 Added information …

Jun 24, 2019:

2:38 PM Ticket #1158 (FASTQ files for external samples should not have the prefix in their names) closed by Nicklas Nordborg
fixed: In 5524: […]
2:38 PM Changeset [5524] by Nicklas Nordborg
Fixes #1158: FASTQ files for external samples should not have the …
11:39 AM Ticket #1158 (FASTQ files for external samples should not have the prefix in their names) created by Nicklas Nordborg
External samples typically have a prefix followed by and underscore …
11:27 AM Changeset [5523] by Nicklas Nordborg
References #1145: Location of data for external RNA The code for …
9:29 AM Changeset [5522] by Nicklas Nordborg
References #1157: Case summary changes due to MIPs pipeline Added …

Jun 20, 2019:

1:37 PM Ticket #1157 (Case summary changes due to MIPs pipeline) created by Nicklas Nordborg
The case summary will happily load all items from the MIPs pipeline …
1:25 PM Changeset [5521] by Nicklas Nordborg
References #1136: MIPs plate lab protocol Added support for pool colors.
12:35 PM Changeset [5520] by Nicklas Nordborg
References #1135: Design MIPs plate wizard Added support for pool colors.
11:36 AM Changeset [5519] by Nicklas Nordborg
References #1130: Import wizard for MIPs aliquot plates Added more …
8:44 AM Changeset [5518] by Nicklas Nordborg
References #1130: Import wizard for MIPs aliquot plates Implemented …

Jun 19, 2019:

3:44 PM Changeset [5517] by Nicklas Nordborg
References #1156: Switch to Java 11 and BASE 3.15 Update Http client. …
2:31 PM Changeset [5516] by Nicklas Nordborg
References #1156: Switch to Java 11 and BASE 3.15 Update JavaMail?.
2:28 PM Changeset [5515] by Nicklas Nordborg
References #1156: Switch to Java 11 and BASE 3.15 Updated Hibernate …
2:19 PM Changeset [5514] by Nicklas Nordborg
References #1156: Switch to Java 11 and BASE 3.15 Updated JSONsimple, …
2:11 PM Changeset [5513] by Nicklas Nordborg
References #1156: Switch to Java 11 and BASE 3.15 Update BASE and …
1:50 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) created by Nicklas Nordborg
See #1147. This also implies updating the other dependencies that have …
1:37 PM Ticket #1155 (Map external data to releases should encrypt the temporary file) closed by Nicklas Nordborg
fixed: In 5512: […]
1:37 PM Changeset [5512] by Nicklas Nordborg
Fixes #1155: Map external data to releases should encrypt the …
1:08 PM Ticket #1123 (Map external data to releases should not include case or specimen ...) closed by Nicklas Nordborg
fixed: In 5511: […]
1:08 PM Changeset [5511] by Nicklas Nordborg
Fixes #1123: Map external data to releases should not include case or …
10:51 AM Ticket #1155 (Map external data to releases should encrypt the temporary file) created by Nicklas Nordborg
It is the same functionality that was implemented in Reggie ticket #1121.

Jun 18, 2019:

3:21 PM Changeset [5510] by Nicklas Nordborg
References #1126: Cohort exporter should support exporting to Excel …
12:48 PM Changeset [5509] by Nicklas Nordborg
References #1126: Cohort exporter should support exporting to Excel …
12:45 PM Changeset [5508] by Nicklas Nordborg
References #1126: Cohort exporter should support exporting to Excel …
8:52 AM Ticket #1154 (Switch to Java 11 and BASE 3.15) closed by Nicklas Nordborg
fixed: In 5507: […]
8:52 AM Changeset [5507] by Nicklas Nordborg
Fixes #1154: Switch to Java 11 and BASE 3.15 Worked fine with just …
8:40 AM Ticket #1118 (Switch to JSON.simple 1.1.1-1) closed by Nicklas Nordborg
fixed: In 5506: […]
8:40 AM Changeset [5506] by Nicklas Nordborg
Fixes #1118: Switch to JSON.simple 1.1.1-1
8:01 AM Ticket #1154 (Switch to Java 11 and BASE 3.15) created by Nicklas Nordborg
See #1147.
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