Timeline



Jun 23, 2021:

3:26 PM Ticket #1322 (Borås should use the '99' referral form types) created by Nicklas Nordborg
Ticket #1309 implemented a referral ID generator. Depending on the …

Jun 18, 2021:

12:50 PM Changeset [6339] by Nicklas Nordborg
References #1299: Import of FASTQ files from external lab Progress …
12:50 PM Changeset [6338] by Nicklas Nordborg
References #1295: Registration of specimen handled by external lab …

Jun 16, 2021:

12:48 PM Tickets #1288,​1302,​1320 batch updated by Nicklas Nordborg
fixed
12:47 PM Changeset [6337] by Nicklas Nordborg
References #1320: Named transactions Fixed in all the remaining wizards.
8:58 AM Changeset [6336] by Nicklas Nordborg
References #1320: Named transactions Fixed in several batch update, …

Jun 15, 2021:

2:51 PM Changeset [6335] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Secondary analysis …
1:46 PM Changeset [6334] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Sequencing wizards".
11:25 AM Changeset [6333] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Library …
9:37 AM Changeset [6332] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Histology wizards".
8:53 AM Ticket #1321 (Warnings in the Tomcat log file) closed by Nicklas Nordborg
fixed: In 6331: […]
8:53 AM Changeset [6331] by Nicklas Nordborg
Fixes #1321: Warnings in the Tomcat log file Removed the references …
8:48 AM Ticket #1321 (Warnings in the Tomcat log file) created by Nicklas Nordborg
Sometimes we get warnings in the Tomcat log file like this: […] …

Jun 14, 2021:

3:59 PM Changeset [6330] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Sample processing …
3:23 PM Changeset [6329] by Nicklas Nordborg
References #1320: Named transactions Fixed in the "Personal …
1:26 PM Changeset [6328] by Nicklas Nordborg
References #1320: Named transactions Fixed in the installation …
11:18 AM Ticket #1314 (Switch to BASE 3.19) closed by Nicklas Nordborg
fixed: In 6327: […]
11:18 AM Changeset [6327] by Nicklas Nordborg
Fixes #1314: Switch to BASE 3.19
11:18 AM Ticket #1320 (Named transactions) created by Nicklas Nordborg
Once #1314 has been fixed it would be nice to use the "Named …
9:06 AM Changeset [6326] by Nicklas Nordborg
Merge Reggie 4.31.3 to the trunk
8:35 AM Changeset [6325] by Nicklas Nordborg
Changes for future release Reggie 4.31.4
8:33 AM Milestone Reggie v4.31.3 completed
Bug fixes and enhancements for Reggie 4.31.2. Revision Log: …
8:32 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.31.3 (diff)
8:32 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.31.3 (diff)
8:30 AM reggie-4.31.3.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.31.3
8:29 AM Changeset [6324] by Nicklas Nordborg
Tagging Reggie 4.31.3
8:28 AM Changeset [6323] by Nicklas Nordborg
Preparing to release Reggie 4.31.3
8:24 AM Ticket #1315 (Support more item types in the outtake wizard) closed by Nicklas Nordborg
fixed

Jun 11, 2021:

3:52 PM Ticket #1316 (Switch to Job Scheduler 1.4) closed by Nicklas Nordborg
fixed: In 6322: […]
3:52 PM Changeset [6322] by Nicklas Nordborg
Fixes #1316: Switch to Job Scheduler 1.4
3:43 PM net.sf.basedb.opengrid edited by Nicklas Nordborg
Fixed incorrect link to changelog for v1.4 (diff)
2:35 PM Changeset [6321] by Nicklas Nordborg
Changes for future release Job scheduler extension 1.5
2:34 PM Milestone Job scheduler extension v1.4 completed
See the Job scheduler extension page for …
2:31 PM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.4 (diff)
2:28 PM opengrid-1.4.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job sceduler 1.4
2:27 PM Changeset [6320] by Nicklas Nordborg
Changes for future release External files support 1.7
2:26 PM Changeset [6319] by Nicklas Nordborg
Tagging Job scheduler extension 1.4
2:25 PM Changeset [6318] by Nicklas Nordborg
Preparing to release Job scheduler extension 1.4
2:22 PM Milestone External files support 1.6 completed
An extension package containing support for additional protocols to …
2:22 PM net.sf.basedb.xfiles edited by Nicklas Nordborg
Released External files support 1.6 (diff)
2:20 PM xfiles-1.6.tar.gz attached to net.sf.basedb.xfiles by Nicklas Nordborg
XFiles 1.6
2:19 PM Changeset [6317] by Nicklas Nordborg
Tagging External files support 1.6
2:18 PM Changeset [6316] by Nicklas Nordborg
Preparing to release External file support 1.6
2:15 PM Ticket #1319 (Update SSH library to version 0.31.0) closed by Nicklas Nordborg
fixed: In 6315: […]
2:15 PM Changeset [6315] by Nicklas Nordborg
Fixes #1319: Update SSH library to version 0.31.0
2:03 PM Ticket #1318 (Switch to BASE 3.18) closed by Nicklas Nordborg
fixed: In 6314: […]
2:03 PM Changeset [6314] by Nicklas Nordborg
Fixes #1318: Switch to BASE 3.18
1:52 PM Changeset [6313] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:51 PM Changeset [6312] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:48 PM Changeset [6311] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:46 PM Changeset [6310] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:45 PM Changeset [6309] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:43 PM Changeset [6308] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:42 PM Changeset [6307] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:39 PM Changeset [6306] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
1:36 PM Changeset [6305] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed links in …
11:04 AM Changeset [6304] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:04 AM Changeset [6303] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:03 AM Changeset [6302] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:02 AM Changeset [6301] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:02 AM Changeset [6300] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:01 AM Changeset [6299] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
11:01 AM Changeset [6298] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
10:59 AM Changeset [6297] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the OTP …
10:58 AM Ticket #1319 (Update SSH library to version 0.31.0) created by Nicklas Nordborg
10:57 AM Ticket #1318 (Switch to BASE 3.18) created by Nicklas Nordborg
10:56 AM Changeset [6296] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
10:56 AM Changeset [6295] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the …
10:50 AM Ticket #1262 (Upgrade ssh library) closed by Nicklas Nordborg
fixed: In 6294: […]
10:50 AM Changeset [6294] by Nicklas Nordborg
Fixes #1262: Upgrade ssh library Updated to 0.31.0.
10:42 AM Changeset [6293] by Nicklas Nordborg
References #1317: base.thep.lu.se is moving to https Fixed in the Job …
10:41 AM Ticket #1261 (Switch to BASE 3.18) closed by Nicklas Nordborg
fixed: In 6292: […]
10:41 AM Changeset [6292] by Nicklas Nordborg
Fixes #1261: Switch to BASE 3.18
10:39 AM Ticket #1317 (base.thep.lu.se is moving to https) created by Nicklas Nordborg
This affects a lot of extension build scripts. Those that have `ant …
10:30 AM Ticket #1262 (Upgrade ssh library) reopened by Nicklas Nordborg
Version 0.31 is now available.
10:30 AM Ticket #1261 (Switch to BASE 3.18) reopened by Nicklas Nordborg
Might as well move to BASE 3.18 since that is the current version.
10:29 AM Ticket #1316 (Switch to Job Scheduler 1.4) created by Nicklas Nordborg
Even if the Slurm cluster is not yet available I think we should …
10:20 AM Ticket #1259 (Add support for Slurm) closed by Nicklas Nordborg
fixed: There are probably still issues with Slurm depending on configuration …
10:16 AM Ticket #1263 (The ScriptBuilder API should perform simple indentation automatically) closed by Nicklas Nordborg
fixed
10:15 AM Ticket #1278 (Improve timeout handling when executing commands on remote server) closed by Nicklas Nordborg
fixed
9:46 AM PluginDownload edited by Nicklas Nordborg
Added Variant Search extension (diff)
9:42 AM PluginDownload edited by Nicklas Nordborg
Released Print package 1.5 (diff)
9:41 AM Changeset [6291] by Nicklas Nordborg
Changes for future release Print package 1.6
9:40 AM Milestone Print package v1.5 completed
See Print package extension page for more …
9:39 AM net.sf.basedb.print edited by Nicklas Nordborg
Released Print package 1.5 (diff)
9:38 AM base-print-1.5.tar.gz attached to net.sf.basedb.print by Nicklas Nordborg
Print package 1.5
9:37 AM Changeset [6290] by Nicklas Nordborg
Tagging Print package 1.5
9:36 AM Changeset [6289] by Nicklas Nordborg
Preparing to release Print package 1.5
9:32 AM Changeset [6288] by Nicklas Nordborg
Changes for future release Variant Search 1.2
9:31 AM Milestone Variant Search v1.1 completed
See Variant Search extension page for …
9:30 AM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.1 (diff)
9:29 AM varsearch-1.1.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.1
9:27 AM Changeset [6287] by Nicklas Nordborg
Tagging Variant Search 1.1
9:26 AM Changeset [6286] by Nicklas Nordborg
Preparing to release Variant Search 1.1
9:24 AM net.sf.basedb.varsearch/using edited by Nicklas Nordborg
Timeout trigger has changed from / to # (diff)
9:13 AM net.sf.basedb.varsearch/install edited by Nicklas Nordborg
Added information about indexing VCF files and the Index Manager (diff)
8:34 AM net.sf.basedb.varsearch/install created by Nicklas Nordborg
Started to write installation instructions for the Variant Search …

Jun 10, 2021:

3:52 PM Changeset [6285] by Nicklas Nordborg
References #1315: Support more item types in the outtake wizard The …
1:50 PM Changeset [6284] by Nicklas Nordborg
References #1315: Support more item types in the outtake wizard Store …
11:39 AM se.lu.onk.BaseFile edited by Jari Häkkinen
(diff)
11:39 AM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
(diff)
11:38 AM se.lu.onk.ReplicateError edited by Jari Häkkinen
(diff)
11:38 AM se.lu.onk.Center edited by Jari Häkkinen
(diff)
11:38 AM net.sf.basedb.normalizers edited by Jari Häkkinen
(diff)
11:37 AM se.lu.onk.VirtualArray edited by Jari Häkkinen
(diff)
11:36 AM net.sf.basedb.agilent edited by Jari Häkkinen
(diff)
11:36 AM se.lu.thep.WeNNI edited by Jari Häkkinen
(diff)
11:00 AM net.sf.basedb.reggie/notes216 edited by Jari Häkkinen
(diff)
11:00 AM net.sf.basedb.reggie/notes32 edited by Jari Häkkinen
(diff)
11:00 AM net.sf.basedb.mev edited by Jari Häkkinen
(diff)
9:24 AM Changeset [6283] by Nicklas Nordborg
References #1315: Support more item types in the outtake wizard The …
8:56 AM Changeset [6282] by Nicklas Nordborg
References #1315: Support more item types in the outtake wizard Added …

Jun 9, 2021:

7:28 PM se.lu.thep.affymetrix edited by Jari Häkkinen
(diff)
7:27 PM se.lu.thep.WeNNI edited by Jari Häkkinen
(diff)
7:26 PM net.sf.basedb.agilent edited by Jari Häkkinen
(diff)
7:26 PM net.sf.basedb.torrent edited by Jari Häkkinen
(diff)
7:25 PM net.sf.basedb.examples.plugins edited by Jari Häkkinen
(diff)
7:25 PM net.sf.basedb.hdfs edited by Jari Häkkinen
(diff)
7:25 PM no.uib.cbu.base.magetabexport edited by Jari Häkkinen
(diff)
7:24 PM net.sf.basedb.brcareg edited by Jari Häkkinen
(diff)
7:24 PM se.lu.onk.VirtualArray edited by Jari Häkkinen
(diff)
7:23 PM net.sf.basedb.normalizers edited by Jari Häkkinen
(diff)
7:23 PM net.sf.basedb.mev edited by Jari Häkkinen
(diff)
7:22 PM net.sf.basedb.examples.webservices edited by Jari Häkkinen
(diff)
7:22 PM net.sf.basedb.ftp edited by Jari Häkkinen
(diff)
7:21 PM net.sf.basedb.illumina edited by Jari Häkkinen
(diff)
7:21 PM net.sf.basedb.examplecode edited by Jari Häkkinen
(diff)
7:20 PM net.sf.basedb.meludi edited by Jari Häkkinen
(diff)
7:20 PM net.sf.basedb.inca edited by Jari Häkkinen
(diff)
7:20 PM net.sf.basedb.xfiles edited by Jari Häkkinen
(diff)
7:19 PM net.sf.basedb.otp edited by Jari Häkkinen
(diff)
7:19 PM net.sf.basedb.yubikey edited by Jari Häkkinen
(diff)
7:19 PM net.sf.basedb.labenv edited by Jari Häkkinen
(diff)
7:18 PM net.sf.basedb.relax edited by Jari Häkkinen
(diff)
7:18 PM net.sf.basedb.opengrid edited by Jari Häkkinen
(diff)
7:17 PM net.sf.basedb.thumbnails edited by Jari Häkkinen
(diff)
7:17 PM net.sf.basedb.print edited by Jari Häkkinen
(diff)
7:16 PM net.sf.basedb.varsearch edited by Jari Häkkinen
(diff)
7:16 PM net.sf.basedb.reggie edited by Jari Häkkinen
(diff)
2:45 PM Ticket #1315 (Support more item types in the outtake wizard) created by Nicklas Nordborg
The outtake wizard currently support RNA and DNA (#913). It would be …
8:24 AM Changeset [6281] by Nicklas Nordborg
References #1288: Select libraries for demuxing in the demux wizard …
8:24 AM Changeset [6280] by Nicklas Nordborg
References #1288: Select libraries for demuxing in the demux wizard …

Jun 7, 2021:

3:56 PM Ticket #1314 (Switch to BASE 3.19) created by Nicklas Nordborg
This will happen some time in the future. The ticket is added here …

Jun 4, 2021:

10:28 AM Ticket #1313 (Varsearch css interferes with BASE CSS) closed by Nicklas Nordborg
fixed: In 6279: […]
10:28 AM Changeset [6279] by Nicklas Nordborg
Fixes #1313: Varsearch css interferes with BASE CSS Added ID selector …
10:07 AM Ticket #1312 (Hide column is not working) closed by Nicklas Nordborg
fixed: In 6278: […]
10:07 AM Changeset [6278] by Nicklas Nordborg
Fixes #1312: Hide column is not working A typo in the method name.
9:01 AM Ticket #1313 (Varsearch css interferes with BASE CSS) created by Nicklas Nordborg
Lazy-loading indicators are missing from the raw bioassay table. This …

Jun 3, 2021:

3:46 PM Changeset [6277] by Nicklas Nordborg
Merge Reggie 4.31.2 to the trunk.
3:22 PM Changeset [6276] by Nicklas Nordborg
Changes for future release Reggie 4.31.3
3:20 PM Milestone Reggie v4.31.2 completed
Bug fixes and enhancements for Reggie 4.31.1. Revision Log: …
3:19 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.31.2 (diff)
3:19 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Fixed link (diff)
3:18 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.31.2 (diff)
3:17 PM reggie-4.31.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.31.2
3:16 PM Ticket #1309 (ID generator for new referral forms) closed by Nicklas Nordborg
fixed
3:13 PM Changeset [6275] by Nicklas Nordborg
Tagging Reggie 4.31.2
3:13 PM Changeset [6274] by Nicklas Nordborg
Preparing to release Reggie 4.31.2

Jun 2, 2021:

9:11 AM Changeset [6273] by Nicklas Nordborg
References #1309: ID generator for new referral forms Remove unused …
9:07 AM Changeset [6272] by Nicklas Nordborg
References #1309: ID generator for new referral forms New entries to …
8:15 AM Ticket #1310 (Implement support for a prefix in the blood referral forms) closed by Nicklas Nordborg
fixed: In 6271: […]
8:15 AM Changeset [6271] by Nicklas Nordborg
Fixes #1310: Implement support for a prefix in the blood referral …

Jun 1, 2021:

2:36 PM Changeset [6270] by Nicklas Nordborg
References #1309: ID generator for new referral forms Change the …
8:37 AM Changeset [6269] by Nicklas Nordborg
References #1309: ID generator for new referral forms The new …

May 31, 2021:

2:20 PM ReadMe_calculation_BAF_Log_R_Ratio.pdf attached to se.lu.onk.IlluminaSNPNormalization by markus
2:19 PM tQN-1.1.2.zip attached to se.lu.onk.IlluminaSNPNormalization by markus
2:17 PM human660w-quad_tQN_clusters.zip attached to se.lu.onk.IlluminaSNPNormalization by markus
2:16 PM human1M-omnia_tQN_clusters.zip attached to se.lu.onk.IlluminaSNPNormalization by markus
2:15 PM se.lu.onk.IlluminaSNPNormalization edited by Jari Häkkinen
(diff)
2:15 PM humanOmni2_5M-quad_tQN_clusters.zip attached to se.lu.onk.IlluminaSNPNormalization by markus
2:13 PM humanOmniExpress_tQN_clusters.zip attached to se.lu.onk.IlluminaSNPNormalization by markus
2:10 PM se.lu.onk.BAFsegmentation edited by Jari Häkkinen
(diff)
2:08 PM SimulatedTumorData.zip attached to se.lu.onk.BAFsegmentation by markus
Simulated Tumor Data
2:06 PM CRL2324_dilutionSeries_BeadStudio.zip attached to se.lu.onk.BAFsegmentation by markus
CRL2324 dilutionSeries BeadStudio?
2:05 PM CRL2324_dilutionSeries_TableExport.zip attached to se.lu.onk.BAFsegmentation by markus
CRL2324 dilutionSeries TableExport?
2:04 PM BAFsegmentation-1.2.0.zip attached to se.lu.onk.BAFsegmentation by markus
BAFsegmentation 1.2.0
2:03 PM BAFsegmentation-2.0pre-snapshot111209.zip attached to se.lu.onk.BAFsegmentation by markus
BAFsegmentation 2.0pre-snapshot 111209
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