Timeline
Jul 5, 2019:
- 1:36 PM Changeset [5541] by
- Refs #1029. FFPE block registration updated in step 3 with support for …
Jul 4, 2019:
- 1:51 PM Changeset [5540] by
-
Refs #1029. Updates due to update of Java version from to
1.8to …
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 Changeset [5539] by
- References #1146: Demux for the MIPs pipeline Added support for …
- 2:28 PM Changeset [5538] by
- References #1146: Demux for the MIPs pipeline Demux parameters has …
- 10:51 AM Changeset [5537] by
- References #1161: Update picard to 2.20 Updated MarkDuplicates step …
- 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 Changeset [5535] by
- References #1161: Update picard to 2.20 Removed all …
- 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 Changeset [5532] by
- References #1162: Add support for using 'M' in the read-string when …
- 11:00 AM Changeset [5531] by
- References #1161: Update picard to 2.20 Implemented a method for …
- 9:43 AM Changeset [5530] by
- References #1162: Add support for using 'M' in the read-string when …
- 9:34 AM Changeset [5529] by
-
References #1161: Update picard to 2.20
Adding the
picard2wrapper … - 9:33 AM Changeset [5528] by
- References #1161: Update picard to 2.20 Updated to the new command …
- 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 …
- 7:45 AM Ticket #1161 (Update picard to 2.20) created by
- 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
- 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 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 Changeset [5526] by
- References #1130, #1135, #1142, #1146. Fixing and getting rid of some …
- 7:54 AM Changeset [5525] by
- 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
- 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 …
- 11:27 AM Changeset [5523] by
- References #1145: Location of data for external RNA The code for …
- 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 Changeset [5521] by
- References #1136: MIPs plate lab protocol Added support for pool colors.
- 12:35 PM Changeset [5520] by
- References #1135: Design MIPs plate wizard Added support for pool colors.
- 11:36 AM Changeset [5519] by
- References #1130: Import wizard for MIPs aliquot plates Added more …
- 8:44 AM Changeset [5518] by
- References #1130: Import wizard for MIPs aliquot plates Implemented …
Jun 19, 2019:
- 3:44 PM Changeset [5517] by
- References #1156: Switch to Java 11 and BASE 3.15 Update Http client. …
- 2:31 PM Changeset [5516] by
- References #1156: Switch to Java 11 and BASE 3.15 Update JavaMail?.
- 2:28 PM Changeset [5515] by
- References #1156: Switch to Java 11 and BASE 3.15 Updated Hibernate …
- 2:19 PM Changeset [5514] by
- References #1156: Switch to Java 11 and BASE 3.15 Updated JSONsimple, …
- 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 Changeset [5510] by
- References #1126: Cohort exporter should support exporting to Excel …
- 12:48 PM Changeset [5509] by
- References #1126: Cohort exporter should support exporting to Excel …
- 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 #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 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 …
- 12:40 PM Ticket #1147 (Switch to Java 11 and BASE 3.15) created by
Jun 14, 2019:
- 8:24 AM Changeset [5495] by
- References #1130: Import wizard for MIPs aliquot plates Added a check …
- 7:45 AM Changeset [5494] by
- References #1146: Demux for the MIPs pipeline The demux auto-confirm …
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