Timeline
Jun 28, 2019:
- 2:35 PM Ticket #1160 (Investigate changes in Picard since our last modified version) closed by
- fixed
- 2:35 PM Ticket #1161 (Update picard to 2.20) closed by
- fixed
- 2:33 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5539: […]
- 2:33 PM Changeset [5539] by
- References #1146: Demux for the MIPs pipeline Added support for …
- 2:28 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5538: […]
- 2:28 PM Changeset [5538] by
- References #1146: Demux for the MIPs pipeline Demux parameters has …
- 10:51 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5537: […]
- 10:51 AM Changeset [5537] by
- References #1161: Update picard to 2.20 Updated MarkDuplicates step …
- 8:47 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5536: […]
- 8:47 AM Changeset [5536] by
- References #1161: Update picard to 2.20 Updated the RNA-seq demux to …
Jun 27, 2019:
- 2:15 PM Ticket #1161 (Update picard to 2.20) updated by
- In 5535: […]
- 2:15 PM Changeset [5535] by
- References #1161: Update picard to 2.20 Removed all …
- 2:00 PM Tickets #1146,1161 batch updated by
- In 5534: […]
- 2:00 PM Changeset [5534] by
- 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
- fixed: In 5533: […]
- 12:43 PM Changeset [5533] by
- 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
- This seems to happen if a sequencing run has already been demuxed more …
- 11:24 AM Ticket #1162 (Add support for using 'M' in the read-string when demuxing) updated by
- In 5532: […]
- 11:24 AM Changeset [5532] by
- References #1162: Add support for using 'M' in the read-string when …
- 11:00 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5531: […]
- 11:00 AM Changeset [5531] by
- References #1161: Update picard to 2.20 Implemented a method for …
- 9:43 AM Ticket #1162 (Add support for using 'M' in the read-string when demuxing) updated by
- In 5530: […]
- 9:43 AM Changeset [5530] by
- References #1162: Add support for using 'M' in the read-string when …
- 9:34 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5529: […]
- 9:34 AM Changeset [5529] by
-
References #1161: Update picard to 2.20
Adding the
picard2wrapper … - 9:33 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5528: […]
- 9:33 AM Changeset [5528] by
- References #1161: Update picard to 2.20 Updated to the new command …
- 9:08 AM Ticket #1161 (Update picard to 2.20) updated by
- In 5527: […]
- 9:08 AM Changeset [5527] by
- 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
- This is needed to handle UMI:s in the MIPs pipeline. It requires the …
- 7:47 AM Ticket #1161 (Update picard to 2.20) updated by
-
Description changed
- 7:45 AM Ticket #1161 (Update picard to 2.20) created by
- http://broadinstitute.github.io/picard/ I think we should manage …
Jun 26, 2019:
- 3:01 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
-
Description changed
- 1:29 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 1 - Item 1, 2 and 3 Fork release 2 - Item 2 …
- 1:23 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 1 - Item 4 The support for FIRST_TILE and MAX_TILES …
- 1:22 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 1 - Item 5 This seems to be fixed in picard.
- 1:05 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 2 - Item 1 See #631 for background information. A …
- 12:21 PM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 4 - Item 1 For background see #742. Picard has made …
- 9:51 AM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork relase 3 - Item 1 We do not use this (in the RNA-seq …
- 9:36 AM Ticket #1160 (Investigate changes in Picard since our last modified version) updated by
- Fork release 5 - Item 1 We do not use AddOrReplaceReadGroups any …
- 9:29 AM Ticket #1160 (Investigate changes in Picard since our last modified version) created by
- 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
- The first task is to make sure that existing items in the RNA-seq …
- 9:28 AM Ticket #1157 (Case summary changes due to MIPs pipeline) updated by
-
Status changed
- 9:28 AM Tickets #1130,1135,1136,1137,1138,1142 batch updated by
- fixed
- 9:25 AM Ticket #1145 (Location of data for external RNA) closed by
- fixed
- 9:25 AM Ticket #1129 (DNA pre-normalization) closed by
- fixed
- 9:24 AM Ticket #1133 (Re-organize the Reggie front page) closed by
- fixed
- 9:05 AM Tickets #1130,1135,1142,1146 batch updated by
- In 5526: […]
- 9:05 AM Changeset [5526] by
- References #1130, #1135, #1142, #1146. Fixing and getting rid of some …
- 7:54 AM Ticket #1154 (Switch to Java 11 and BASE 3.15) updated by
- In 5525: […]
- 7:54 AM Changeset [5525] by
- References #1154: Switch to Java 11 and BASE 3.15 Added information …
Jun 24, 2019:
- 4:13 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by
- Design update: * As the result of discussions at the …
- 2:38 PM Ticket #1158 (FASTQ files for external samples should not have the prefix in their names) closed by
- fixed: In 5524: […]
- 2:38 PM Changeset [5524] by
- 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
- External samples typically have a prefix followed by and underscore …
- 11:28 AM Ticket #1145 (Location of data for external RNA) updated by
- In 5523: […]
- 11:27 AM Changeset [5523] by
- References #1145: Location of data for external RNA The code for …
- 9:32 AM Ticket #1145 (Location of data for external RNA) updated by
-
Status, Milestone changed
- 9:29 AM Ticket #1157 (Case summary changes due to MIPs pipeline) updated by
- In 5522: […]
- 9:29 AM Changeset [5522] by
- 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
- The case summary will happily load all items from the MIPs pipeline …
- 1:25 PM Ticket #1136 (MIPs plate lab protocol) updated by
- In 5521: […]
- 1:25 PM Changeset [5521] by
- References #1136: MIPs plate lab protocol Added support for pool colors.
- 12:35 PM Ticket #1135 (Design MIPs plate wizard) updated by
- In 5520: […]
- 12:35 PM Changeset [5520] by
- References #1135: Design MIPs plate wizard Added support for pool colors.
- 11:36 AM Ticket #1130 (Import wizard for MIPs aliquot plates) updated by
- In 5519: […]
- 11:36 AM Changeset [5519] by
- References #1130: Import wizard for MIPs aliquot plates Added more …
- 8:44 AM Ticket #1130 (Import wizard for MIPs aliquot plates) updated by
- In 5518: […]
- 8:44 AM Changeset [5518] by
- References #1130: Import wizard for MIPs aliquot plates Implemented …
Jun 19, 2019:
- 3:44 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) updated by
- In 5517: […]
- 3:44 PM Changeset [5517] by
- References #1156: Switch to Java 11 and BASE 3.15 Update Http client. …
- 2:31 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) updated by
- In 5516: […]
- 2:31 PM Changeset [5516] by
- References #1156: Switch to Java 11 and BASE 3.15 Update JavaMail.
- 2:28 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) updated by
- In 5515: […]
- 2:28 PM Changeset [5515] by
- References #1156: Switch to Java 11 and BASE 3.15 Updated Hibernate …
- 2:19 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) updated by
- In 5514: […]
- 2:19 PM Changeset [5514] by
- References #1156: Switch to Java 11 and BASE 3.15 Updated JSONsimple, …
- 2:11 PM Ticket #1156 (Switch to Java 11 and BASE 3.15) updated by
- In 5513: […]
- 2:11 PM Changeset [5513] by
- 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
- 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
- fixed: In 5512: […]
- 1:37 PM Changeset [5512] by
- 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
- fixed: In 5511: […]
- 1:08 PM Changeset [5511] by
- 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
- It is the same functionality that was implemented in Reggie ticket #1121.
Jun 18, 2019:
- 3:21 PM Ticket #1126 (Cohort exporter should support exporting to Excel file) updated by
- In 5510: […]
- 3:21 PM Changeset [5510] by
- References #1126: Cohort exporter should support exporting to Excel …
- 12:48 PM Ticket #1126 (Cohort exporter should support exporting to Excel file) updated by
- In 5509: […]
- 12:48 PM Changeset [5509] by
- References #1126: Cohort exporter should support exporting to Excel …
- 12:45 PM Ticket #1126 (Cohort exporter should support exporting to Excel file) updated by
- In 5508: […]
- 12:45 PM Changeset [5508] by
- References #1126: Cohort exporter should support exporting to Excel …
- 8:52 AM Ticket #1154 (Switch to Java 11 and BASE 3.15) closed by
- fixed: In 5507: […]
- 8:52 AM Changeset [5507] by
- 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
- fixed: In 5506: […]
- 8:40 AM Changeset [5506] by
- 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
- See #1147.
Jun 17, 2019:
- 2:49 PM net.sf.basedb.opengrid edited by
- Added entry for future release Opengrid extension 1.3 (diff)
- 2:48 PM Ticket #1152 (Switch to Java 11 and BASE 3.15) closed by
- fixed: In 5505: […]
- 2:48 PM Changeset [5505] by
- Fixes #1152: Switch to Java 11 and BASE 3.15 Worked fine with just …
- 2:42 PM Ticket #1117 (Switch to JSON.simple 1.1.1-1) closed by
- fixed: In 5504: […]
- 2:42 PM Changeset [5504] by
- Fixes #1117: Switch to JSON.simple 1.1.1-1
- 2:39 PM Ticket #1153 (Update SSH library) closed by
- fixed: In 5503: […]
- 2:39 PM Changeset [5503] by
- Fixes #1153: Update SSH library Updated to version 0.27.0
- 2:35 PM Ticket #1152 (Switch to Java 11 and BASE 3.15) updated by
-
Type, Component, Milestone changed
- 2:35 PM Ticket #1153 (Update SSH library) created by
- The latest version is 0.27: …
- 2:34 PM Ticket #1152 (Switch to Java 11 and BASE 3.15) created by
- See #1147
- 2:31 PM net.sf.basedb.xfiles edited by
- Added entry for future release X-files 1.5 (diff)
- 2:30 PM Ticket #1150 (Switch to Java 11 and BASE 3.15) closed by
- fixed: In 5502: […]
- 2:30 PM Changeset [5502] by
- Fixes #1150: Switch to Java 11 and BASE 3.15 Worked fine with just …
- 2:25 PM Ticket #1151 (Update SSH library) closed by
- fixed: In 5501: […]
- 2:25 PM Changeset [5501] by
- Fixes #1151: Update SSH library The new version is no 0.27.0.
- 2:17 PM Ticket #1151 (Update SSH library) created by
- The latest version is 0.27: …
- 2:16 PM Ticket #1150 (Switch to Java 11 and BASE 3.15) created by
- See #1147.
- 1:39 PM net.sf.basedb.yubikey edited by
- Added entry for future release Yubikey login 1.6 (diff)
- 1:37 PM Ticket #1148 (Switch to Java 11 and BASE 3.15) closed by
- fixed: In 5500: […]
- 1:37 PM Changeset [5500] by
- Fixes #1148: Switch to Java 11 and BASE 3.15 Worked fine with just …
- 1:36 PM Ticket #1149 (Update Yubico client API) updated by
- In 5499: […]
- 1:36 PM Changeset [5499] by
- References #1149: Update Yubico client API The class path must also …
- 1:25 PM Ticket #1149 (Update Yubico client API) closed by
- fixed: In 5498: […]
- 1:25 PM Changeset [5498] by
- Fixes #1149: Update Yubico client API
- 1:21 PM Ticket #1149 (Update Yubico client API) created by
- The latest version is 3.0.5 which claims to have some fixes for Java …
- 1:12 PM Ticket #1116 (Switch to JSON.simple 1.1.1-1) closed by
- fixed: In 5497: […]
- 1:12 PM Changeset [5497] by
- Fixes #1116: Switch to JSON.simple 1.1.1-1
- 1:09 PM Ticket #1148 (Switch to Java 11 and BASE 3.15) created by
- See #1147.
- 1:08 PM net.sf.basedb.otp edited by
- Added entry for future release OTP login 1.3 (diff)
- 1:06 PM Ticket #1147 (Switch to Java 11 and BASE 3.15) closed by
- fixed: In 5496: […]
- 1:06 PM Changeset [5496] by
- Fixes #1147: Switch to Java 11 and BASE 3.15 Worked fine with just …
- 1:06 PM Ticket #1147 (Switch to Java 11 and BASE 3.15) updated by
-
Owner, Component changed
- 12:42 PM Ticket #1147 (Switch to Java 11 and BASE 3.15) updated by
-
Summary changed
- 12:40 PM Ticket #1147 (Switch to Java 11 and BASE 3.15) created by
Jun 14, 2019:
- 8:24 AM Ticket #1130 (Import wizard for MIPs aliquot plates) updated by
- In 5495: […]
- 8:24 AM Changeset [5495] by
- References #1130: Import wizard for MIPs aliquot plates Added a check …
- 7:45 AM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5494: […]
- 7:45 AM Changeset [5494] by
- References #1146: Demux for the MIPs pipeline The demux auto-confirm …
Jun 13, 2019:
- 2:16 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5493: […]
- 2:16 PM Changeset [5493] by
- References #1146: Demux for the MIPs pipeline Added a wizard for …
- 1:41 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5492: […]
- 1:41 PM Changeset [5492] by
- References #1146: Demux for the MIPs pipeline Re-factored a lot of …
- 8:49 AM Tickets #1142,1146 batch updated by
- In 5491: […]
- 8:49 AM Changeset [5491] by
- References #1146 and #1142. Auto-confirmation of a MIPs sequencing …
- 8:18 AM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5490: […]
- 8:18 AM Changeset [5490] by
- References #1146: Demux for the MIPs pipeline Implemented job …
Jun 12, 2019:
- 4:02 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5489: […]
- 4:02 PM Changeset [5489] by
- References #1146: Demux for the MIPs pipeline Added a second …
- 2:18 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5488: […]
- 2:18 PM Changeset [5488] by
- References #1142: Create MIPs flow cell and start/end/confirm …
- 1:44 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5487: […]
- 1:44 PM Changeset [5487] by
- References #1146: Demux for the MIPs pipeline Implemented parts of …
- 9:59 AM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5486: […]
- 9:59 AM Changeset [5486] by
- References #1146: Demux for the MIPs pipeline Started to prepare for …
- 8:34 AM Tickets #1142,1146 batch updated by
- In 5485: […]
- 8:34 AM Changeset [5485] by
-
References #1146 and #1142. Added role
MIPsSecondayAnalysis.
Jun 11, 2019:
- 4:20 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5484: […]
- 4:19 PM Changeset [5484] by
- References #1142: Create MIPs flow cell and start/end/confirm …
- 3:35 PM Tickets #1130,1135,1136 batch updated by
- In 5483: […]
- 3:35 PM Changeset [5483] by
- References #1130, #1135, #1136. Synchronized some missing styles and …
- 1:14 PM Ticket #1129 (DNA pre-normalization) updated by
- In 5482: […]
- 1:14 PM Changeset [5482] by
- References #1129: DNA pre-normalization Pre-normalized DNA plates …
- 1:07 PM Tickets #1130,1135,1136 batch updated by
- In 5481: […]
- 1:07 PM Changeset [5481] by
- References #1130, #1135, #1136. Introduced soft line-breaks in sample …
Jun 10, 2019:
- 2:49 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5480: […]
- 2:49 PM Changeset [5480] by
- References #1146: Demux for the MIPs pipeline Added "Pipeline" …
- 2:32 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
- In 5479: […]
- 2:32 PM Changeset [5479] by
- References #1146: Demux for the MIPs pipeline The existing demux …
- 1:01 PM Ticket #1146 (Demux for the MIPs pipeline) updated by
-
Status changed
- 1:01 PM Ticket #1146 (Demux for the MIPs pipeline) created by
- This is probably similar to the RNAseq demux in some sense, but …
- 12:59 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5478: […]
- 12:59 PM Changeset [5478] by
- References #1142: Create MIPs flow cell and start/end/confirm …
- 10:44 AM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5477: […]
- 10:44 AM Changeset [5477] by
- References #1142: Create MIPs flow cell and start/end/confirm …
- 10:41 AM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
-
Summary changed
- 9:50 AM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5476: […]
- 9:50 AM Changeset [5476] by
- References #1142: Create MIPs flow cell and start sequencing Updated …
Jun 5, 2019:
- 4:21 PM Ticket #1144 (Line numbers in the INCA report files seems to be data lines and not ...) closed by
- fixed
- 4:21 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5475: […]
- 4:21 PM Changeset [5475] by
- References #1142: Create MIPs flow cell and start sequencing The …
- 4:14 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5474: […]
- 4:14 PM Changeset [5474] by
- References #1142: Create MIPs flow cell and start sequencing Added a …
- 2:07 PM Ticket #1138 (MIPs pooling) updated by
- In 5473: […]
- 2:07 PM Changeset [5473] by
- References #1138: MIPs pooling Register any-to-any links from pools …
- 1:26 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5472: […]
- 1:26 PM Changeset [5472] by
- References #1142: Create MIPs flow cell and start sequencing Counters …
- 1:11 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5471: […]
- 1:11 PM Changeset [5471] by
- References #1142: Create MIPs flow cell and start sequencing Manual …
- 10:44 AM Ticket #1145 (Location of data for external RNA) created by
- The code that generates a folder location from an item name doesn't …
- 8:28 AM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5470: […]
- 8:28 AM Changeset [5470] by
- References #1142: Create MIPs flow cell and start sequencing …
Jun 4, 2019:
- 3:44 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5469: […]
- 3:44 PM Changeset [5469] by
- References #1142: Create MIPs flow cell and start sequencing Added …
- 2:52 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by
- In 5468: […]
- 2:52 PM Changeset [5468] by
- Refs #1029. Updates of BASE method calls due to update of BASE version …
- 2:51 PM Ticket #1143 (INCA import fails if the last column is empty in one or more rows) closed by
- fixed: In 5467: […]
- 2:51 PM Changeset [5467] by
- Fixes #1143: INCA import fails if the last column is empty in one or …
- 2:48 PM Ticket #1144 (Line numbers in the INCA report files seems to be data lines and not ...) updated by
- Fixed in [5466]. Also fixes a similar problem with column numbers.
- 2:46 PM Changeset [5466] by
- 2:35 PM Ticket #1144 (Line numbers in the INCA report files seems to be data lines and not ...) created by
- They differ with 1 from the actual line number in the file.
- 2:33 PM Ticket #1143 (INCA import fails if the last column is empty in one or more rows) created by
- In the report for excluded lines there is a message that some rows has …
- 2:31 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by
- In 5465: […]
- 2:31 PM Changeset [5465] by
-
Refs #1029. Updates due to update of BASE version to "
3.15.0". 1. … - 2:28 PM Ticket #1130 (Import wizard for MIPs aliquot plates) updated by
- In 5464: […]
- 2:28 PM Changeset [5464] by
- References #1130: Import wizard for MIPs aliquot plates The importer …
Jun 3, 2019:
- 12:56 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5463: […]
- 12:56 PM Changeset [5463] by
- References #1142: Create MIPs flow cell and start sequencing Remove …
- 12:55 PM Ticket #1142 (Create MIPs flow cell and start/end/confirm sequencing) updated by
- In 5462: […]
- 12:55 PM Changeset [5462] by
- References #1142: Create MIPs flow cell and start sequencing …
- 11:05 AM Ticket #1130 (Import wizard for MIPs aliquot plates) updated by
- In 5461: […]
- 11:05 AM Changeset [5461] by
- References #1130: Import wizard for MIPs aliquot plates Changed the …
- 9:22 AM Ticket #1135 (Design MIPs plate wizard) updated by
- In 5460: […]
- 9:22 AM Changeset [5460] by
- References #1135: Design MIPs plate wizard Added a MIPS pool row to …
Note:
See TracTimeline
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