Timeline



May 4, 2022:

2:07 PM Changeset [6726] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …
11:18 AM Changeset [6725] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …
11:07 AM Changeset [6724] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …
9:41 AM Changeset [6723] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …
7:33 AM Changeset [6722] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …

May 3, 2022:

2:24 PM Changeset [6721] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …
9:25 AM Changeset [6720] by Nicklas Nordborg
References #1390: Updates to wizards that assume tubes are marked with …

May 2, 2022:

1:49 PM Changeset [6719] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
9:37 AM Changeset [6718] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …

Apr 29, 2022:

2:22 PM Ticket #1393 (Release exporter changes due to Oncoarray data) created by Nicklas Nordborg
In ticket #1346, we added data from Oncoarray SNP chips to lorry. A …
2:09 PM Tickets #585,​586 batch updated by Nicklas Nordborg
wontfix: This is not needed since sequencing machines do clustering as part of …
2:07 PM Ticket #476 (Get list of blood samples where at least one RNA extract exists) closed by Nicklas Nordborg
worksforme: This should not be too complicated with the help of BASE features that …
1:41 PM Changeset [6717] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
12:52 PM Changeset [6716] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
11:13 AM Changeset [6715] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
9:20 AM Changeset [6714] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …

Apr 28, 2022:

9:43 AM Ticket #1391 (Implement a way to insert a "Reggie was updated..." log entry when ...) closed by Nicklas Nordborg
fixed: In 6713: […]
9:43 AM Changeset [6713] by Nicklas Nordborg
Fixes #1391: Implement a way to insert a "Reggie was updated..." log …
9:07 AM Ticket #1392 (The default configuration is missing a JAVA_HOME declaration in the ...) closed by Nicklas Nordborg
fixed: In 6712: […]
9:07 AM Changeset [6712] by Nicklas Nordborg
Fixes #1392: The default configuration is missing a JAVA_HOME …
9:05 AM Ticket #1392 (The default configuration is missing a JAVA_HOME declaration in the ...) created by Nicklas Nordborg
Without this, vardict is selecting the first java that it can find on …

Apr 27, 2022:

2:55 PM Ticket #1391 (Implement a way to insert a "Reggie was updated..." log entry when ...) created by Nicklas Nordborg
The "Installation wizard" can always be used to check if a new Reggie …
2:50 PM Ticket #1390 (Updates to wizards that assume tubes are marked with item name) created by Nicklas Nordborg
Samples that have been handled externally and then transferred to the …
2:41 PM Changeset [6711] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
11:48 AM Changeset [6710] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
11:36 AM Changeset [6709] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
11:04 AM Changeset [6708] by Nicklas Nordborg
Changes for future release Job scheduler 1.7
11:03 AM Milestone Job scheduler extension v1.6 completed
See the Job scheduler extension page for …
11:02 AM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.6 (diff)
11:00 AM opengrid-1.6.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job scheduler 1.6
10:58 AM Changeset [6707] by Nicklas Nordborg
Tagging Job scheduler 1.6
10:57 AM Changeset [6706] by Nicklas Nordborg
Preparing to release Job scheduler 1.6
9:46 AM Ticket #1389 (TMPDIR is re-defined twice when starting jobs) closed by Nicklas Nordborg
fixed: In 6705: […]
9:46 AM Changeset [6705] by Nicklas Nordborg
Fixes #1389: TMPDIR is re-defined twice when starting jobs No …
9:37 AM Ticket #1389 (TMPDIR is re-defined twice when starting jobs) created by Nicklas Nordborg
I found a problem when a cluster was configured with default value for …

Apr 26, 2022:

2:42 PM Changeset [6704] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
1:45 PM Changeset [6703] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
1:38 PM Changeset [6702] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
1:19 PM Changeset [6701] by Nicklas Nordborg
References #1388: Updates to registration of specimen handled by …
11:32 AM Ticket #1388 (Updates to registration of specimen handled by external lab) created by Nicklas Nordborg
There is a new test file with some changes that should take us a bit …
10:33 AM Ticket #1364 (Update to BASE 3.19) closed by Nicklas Nordborg
fixed
10:32 AM Changeset [6700] by Nicklas Nordborg
References #1365: Update to Lucene 9 Display Lucene version on the …
9:37 AM Ticket #1365 (Update to Lucene 9) closed by Nicklas Nordborg
fixed: In 6699: […]
9:37 AM Changeset [6699] by Nicklas Nordborg
Fixes #1365: Update to Lucene 9 Updated to Lucene 9.1

Apr 25, 2022:

11:19 AM Changeset [6698] by Nicklas Nordborg
Changes for future release Reggie 4.39
11:16 AM Milestone Reggie v4.38 completed
See Reggie extension page for more information.
11:15 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.38 (diff)
11:15 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.38 (diff)
11:12 AM reggie-4.38.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.38
11:11 AM Changeset [6697] by Nicklas Nordborg
Tagging Reggie 4.38
11:10 AM Changeset [6696] by Nicklas Nordborg
Preparing to release Reggie 4.38.
8:18 AM Changeset [6695] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 22, 2022:

10:58 AM Ticket #1374 (Implement support for running jobs in a Singularity container) closed by Nicklas Nordborg
fixed
9:32 AM Changeset [6694] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
8:52 AM Changeset [6693] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 21, 2022:

1:27 PM Changeset [6692] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
10:02 AM Changeset [6691] by Nicklas Nordborg
Changes for future release Job scheduler extension 1.6
10:01 AM Milestone Job scheduler extension v1.5 completed
See the Job scheduler extension page for …
10:00 AM PluginDownload edited by Nicklas Nordborg
Released Job scheduler extension 1.5 (diff)
9:59 AM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.5 (diff)
9:56 AM opengrid-1.5.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job scheduler 1.5
9:54 AM Changeset [6690] by Nicklas Nordborg
Tagging Job scheduler extension 1.5
9:53 AM Changeset [6689] by Nicklas Nordborg
Preparing to release Job scheduler extension 1.5
9:37 AM Changeset [6688] by Nicklas Nordborg
References #1369: Implement support for starting jobs without a queue …
9:33 AM Ticket #1375 (Changes that are needed or useful for running jobs inside a container) closed by Nicklas Nordborg
fixed
9:22 AM net.sf.basedb.opengrid/install edited by Nicklas Nordborg
Update documentation for Job scheduler 1.5 (diff)
9:13 AM Ticket #1369 (Implement support for starting jobs without a queue system) closed by Nicklas Nordborg
fixed
9:09 AM Changeset [6687] by Nicklas Nordborg
References #1384: Add a (increasing) delay when submitting multiple …
9:07 AM Changeset [6686] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 20, 2022:

2:46 PM Changeset [6685] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
2:11 PM Ticket #1387 (Reload reggie-config.xml) closed by Nicklas Nordborg
fixed: In 6684: […]
2:11 PM Changeset [6684] by Nicklas Nordborg
Fixes #1387: Reload reggie-config.xml
1:19 PM Changeset [6683] by Nicklas Nordborg
References #1387: Reload reggie-config.xml Added a method …
1:14 PM Ticket #1387 (Reload reggie-config.xml) created by Nicklas Nordborg
This can currently be done via the web interface on the Open Grid …
11:15 AM Changeset [6682] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
10:47 AM Changeset [6681] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
9:09 AM Changeset [6680] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 19, 2022:

1:18 PM Changeset [6679] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
8:09 AM Ticket #1386 (Remove the genseq_check_illumina_dir.pl program from the "Check data ...) closed by Nicklas Nordborg
fixed: In 6678: […]
8:09 AM Changeset [6678] by Nicklas Nordborg
Fixes #1386: Remove the genseq_check_illumina_dir.pl program from the …

Apr 14, 2022:

1:51 PM Ticket #1386 (Remove the genseq_check_illumina_dir.pl program from the "Check data ...) created by Nicklas Nordborg
We do not need this anymore and it will be a lot more complicated to …
1:18 PM Changeset [6677] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 13, 2022:

9:04 AM Changeset [6676] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
9:02 AM Changeset [6675] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …

Apr 11, 2022:

11:35 AM Ticket #1385 (Add a (increasing) delay when submitting multiple jobs in a batch) closed by Nicklas Nordborg
fixed: In 6674: […]
11:35 AM Changeset [6674] by Nicklas Nordborg
Fixes #1385: Add a (increasing) delay when submitting multiple jobs in …
11:31 AM Ticket #1385 (Add a (increasing) delay when submitting multiple jobs in a batch) created by Nicklas Nordborg
This is related to #1384. For most situations the implementation in …
9:31 AM Changeset [6673] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
9:28 AM Ticket #1384 (Add a (increasing) delay when submitting multiple jobs in a batch) closed by Nicklas Nordborg
fixed: In 6672: […]
9:28 AM Changeset [6672] by Nicklas Nordborg
Fixes #1384: Add a (increasing) delay when submitting multiple jobs in …

Apr 8, 2022:

1:13 PM Ticket #1384 (Add a (increasing) delay when submitting multiple jobs in a batch) created by Nicklas Nordborg
When submitting multiple jobs at the same time and the cluster has a …
7:21 AM Ticket #1383 (Display number of FASTQ pairs waiting in the "Import gateway" on the ...) closed by Nicklas Nordborg
fixed: Fixed in [6671]

Apr 7, 2022:

9:04 AM Changeset [6671] by Nicklas Nordborg
8:57 AM Ticket #1383 (Display number of FASTQ pairs waiting in the "Import gateway" on the ...) created by Nicklas Nordborg
On the index page there is already a counter for the number of JSON …
8:23 AM Ticket #1382 (Batch toggle/set/clear checkboxes in secondary analysis confirmation ...) closed by Nicklas Nordborg
fixed: In 6670: […]
8:23 AM Changeset [6670] by Nicklas Nordborg
Fixes #1382: Batch toggle/set/clear checkboxes in secondary analysis …
7:28 AM Ticket #1382 (Batch toggle/set/clear checkboxes in secondary analysis confirmation ...) created by Nicklas Nordborg
The confirmation wizards in the secondary analysis typically have …

Apr 6, 2022:

10:00 AM Changeset [6669] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
9:52 AM Changeset [6668] by Nicklas Nordborg
References #1375: Changes that are needed or useful for running jobs …

Apr 5, 2022:

9:41 AM Changeset [6667] by Nicklas Nordborg
References #1375: Changes that are needed or useful for running jobs …
9:36 AM Changeset [6666] by Nicklas Nordborg
References #1375: Changes that are needed or useful for running jobs …
9:33 AM Changeset [6665] by Nicklas Nordborg
References #1374: Implement support for running jobs in a Singularity …
9:00 AM Ticket #1381 (Manually confirming a variant call analysis doesn't add the raw ...) closed by Nicklas Nordborg
fixed: In 6664: […]
9:00 AM Changeset [6664] by Nicklas Nordborg
Fixes #1381: Manually confirming a variant call analysis doesn't add …
8:57 AM Ticket #1381 (Manually confirming a variant call analysis doesn't add the raw ...) created by Nicklas Nordborg
The next step after variant calling is to do targeted genotyping. This …
Note: See TracTimeline for information about the timeline view.