Timeline



Dec 9, 2022:

2:05 PM Ticket #1430 (Change default group permissions for archived JSON and FASTQ files) closed by Nicklas Nordborg
fixed: In 6952: […]
2:04 PM Changeset [6952] by Nicklas Nordborg
Fixes #1430: Change default group permissions for archived JSON and …
2:03 PM Ticket #1430 (Change default group permissions for archived JSON and FASTQ files) created by Nicklas Nordborg
The default group permissions was removed completely in #1425. I think …
12:01 PM Ticket #1429 (Adjust Lysate.Used quantity so that it is not more than ...) closed by Nicklas Nordborg
fixed: In 6951: […]
12:01 PM Changeset [6951] by Nicklas Nordborg
Fixes #1429: Adjust Lysate.Used quantity so that it is not more than …
11:44 AM Ticket #1429 (Adjust Lysate.Used quantity so that it is not more than ...) created by Nicklas Nordborg
There is already a warning about this, but we should also adjust the …
9:37 AM Ticket #1428 (Allow some information to be different when there are multiple ...) closed by Nicklas Nordborg
fixed: In 6950: […]
9:37 AM Changeset [6950] by Nicklas Nordborg
Fixes #1428: Allow some information to be different when there are …
9:34 AM Ticket #1428 (Allow some information to be different when there are multiple ...) created by Nicklas Nordborg
When importing specimen information from JSON files, there is the …
9:21 AM Changeset [6949] by Nicklas Nordborg
References #1427: Make use of the header information in FASTQ files …

Dec 8, 2022:

2:05 PM Changeset [6948] by Nicklas Nordborg
References #1427: Make use of the header information in FASTQ files …
1:28 PM Changeset [6947] by Nicklas Nordborg
References #1427: Make use of the header information in FASTQ files …
12:51 PM Ticket #1427 (Make use of the header information in FASTQ files) created by Nicklas Nordborg
The import wizard for external JSON/FASTQ could maybe use some …

Dec 6, 2022:

3:56 PM Changeset [6946] by Nicklas Nordborg
Merge Reggie 4.41.1 to the trunk.
3:52 PM Milestone Reggie v4.41.1 completed
Bug fixes and enhancements for Reggie 4.41. Revision Log: …
3:52 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.41.1 (diff)
3:51 PM reggie-4.41.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.41.1
3:49 PM Changeset [6945] by Nicklas Nordborg
Tagging Reggie 4.41.1
3:48 PM Changeset [6944] by Nicklas Nordborg
Preparing to release Reggie 4.41.1
2:43 PM Tickets #1425,​1426 batch updated by Nicklas Nordborg
fixed
2:34 PM Changeset [6943] by Nicklas Nordborg
References #1426: Warn/fix unreasonble values for RNA remaining …
1:24 PM Changeset [6942] by Nicklas Nordborg
References #1425: JSON and FASTQ files that are stored in the …
1:05 PM Changeset [6941] by Nicklas Nordborg
References #1425: JSON and FASTQ files that are stored in the …
12:01 PM Ticket #1426 (Warn/fix unreasonble values for RNA remaining quantity in JSON files) created by Nicklas Nordborg
The JSON files that are imported by the "Import externally processed …
11:45 AM Ticket #1425 (JSON and FASTQ files that are stored in the ImportArchive should be ...) created by Nicklas Nordborg
The JSON file is copied by the "Import externally processed samles" …
11:42 AM Ticket #1424 (Incorrect path to UCSC_hg38_knownGenes_22sep2014.gtf) closed by Nicklas Nordborg
fixed: In 6940: […]
11:42 AM Changeset [6940] by Nicklas Nordborg
Fixes #1424: Incorrect path to UCSC_hg38_knownGenes_22sep2014.gtf
11:35 AM Ticket #1424 (Incorrect path to UCSC_hg38_knownGenes_22sep2014.gtf) created by Nicklas Nordborg
The default configuration for the legacy pipeline on the Slurm cluster …
8:37 AM Ticket #1423 (NullPointerException when starting Methylation beta-analysis) closed by Nicklas Nordborg
fixed: In 6939: […]
8:37 AM Changeset [6939] by Nicklas Nordborg
Fixes #1423: NullPointerException? when starting Methylation beta-analysis

Dec 5, 2022:

2:53 PM Changeset [6938] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.41
2:51 PM Ticket #1423 (NullPointerException when starting Methylation beta-analysis) created by Nicklas Nordborg
Selecting items, and job options works, but the final registration …
9:57 AM Changeset [6937] by Nicklas Nordborg
Changes for future relase Reggie 4.42
9:55 AM Milestone Reggie v4.41 completed
See Reggie extension page for more information.
9:54 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.41 (diff)
9:54 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.41 (diff)
9:52 AM reggie-4.41.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.41
9:51 AM Changeset [6936] by Nicklas Nordborg
Tagging Reggie 4.41
9:50 AM Changeset [6935] by Nicklas Nordborg
Preparing to release Reggie 4.41
9:48 AM Ticket #1420 (Updates to registration of specimen handled by external lab) closed by Nicklas Nordborg
fixed
9:43 AM Ticket #1419 (Methylation beta-analysis wizard) closed by Nicklas Nordborg
fixed
9:43 AM Ticket #1418 (Implement support for methylation data) closed by Nicklas Nordborg
fixed
9:42 AM Ticket #1422 (Add default configuration options for the new Slurm cluster) closed by Nicklas Nordborg
fixed
9:33 AM Changeset [6934] by Nicklas Nordborg
References #1422: Add default configuration options for the new Slurm …
9:08 AM Changeset [6933] by Nicklas Nordborg
References #1422: Add default configuration options for the new Slurm …
8:37 AM Changeset [6932] by Nicklas Nordborg
References #1422: Add default configuration options for the new Slurm …
8:33 AM Changeset [6931] by Nicklas Nordborg
References #1422: Add default configuration options for the new Slurm …
7:47 AM Changeset [6930] by Nicklas Nordborg
References #1422: Add default configuration options for the new Slurm …
7:31 AM Ticket #1422 (Add default configuration options for the new Slurm cluster) created by Nicklas Nordborg
This should be usable now and we should enable it in Reggie so that we …

Dec 2, 2022:

2:24 PM Changeset [6929] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:48 PM Changeset [6928] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:46 PM Changeset [6927] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:44 PM Changeset [6926] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
12:57 PM Changeset [6925] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
12:02 PM Changeset [6924] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:35 AM Changeset [6923] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:06 AM Changeset [6922] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
8:44 AM Changeset [6921] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Dec 1, 2022:

3:48 PM Changeset [6920] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:47 PM Changeset [6919] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:32 PM Changeset [6918] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:16 PM Changeset [6917] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:53 AM Changeset [6916] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:51 AM Changeset [6915] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
7:53 AM Changeset [6914] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Nov 30, 2022:

2:42 PM Changeset [6913] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:09 PM Changeset [6912] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:08 PM Changeset [6911] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:43 AM Changeset [6910] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:42 AM Changeset [6909] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:12 AM Changeset [6908] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:11 AM Changeset [6907] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
8:55 AM Changeset [6906] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
8:35 AM Changeset [6905] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Nov 29, 2022:

3:35 PM Changeset [6904] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:24 PM Changeset [6903] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:17 PM Changeset [6902] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
2:02 PM Changeset [6901] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:10 PM Changeset [6900] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
11:12 AM Changeset [6899] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
10:17 AM Changeset [6898] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:48 AM Changeset [6897] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Nov 28, 2022:

3:24 PM Changeset [6896] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Nov 25, 2022:

3:59 PM Changeset [6895] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
1:55 PM Changeset [6894] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:25 AM Changeset [6893] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …

Nov 24, 2022:

1:48 PM Milestone Reggie v4.40.2 completed
Bug fixes and enhancements for Reggie 4.40.1. Revision Log: …
1:48 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.40.2 (diff)
1:47 PM reggie-4.40.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.40.2
1:46 PM Changeset [6892] by Nicklas Nordborg
Merge Reggie 4.40.2 to the trunk.
1:01 PM Changeset [6891] by Nicklas Nordborg
Tagging Reggie 4.40.2
1:01 PM Changeset [6890] by Nicklas Nordborg
Preparing to release Reggie 4.40.2
12:59 PM Ticket #1421 (NullPointerException in extraction registration wizard) closed by Nicklas Nordborg
fixed: In 6889: […]
12:59 PM Changeset [6889] by Nicklas Nordborg
Fixes #1421: NullPointerException? in extraction registration wizard …
12:46 PM Ticket #1421 (NullPointerException in extraction registration wizard) created by Nicklas Nordborg
This happened in the second step: […] The log file contains a …
9:24 AM Changeset [6888] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:17 AM Changeset [6887] by Nicklas Nordborg
References #1420: Updates to registration of specimen handled by …
9:07 AM Ticket #1420 (Updates to registration of specimen handled by external lab) created by Nicklas Nordborg
See #1349, #1347 and #1295 for background information about earlier …
8:38 AM Changeset [6886] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Adding a reference …
8:35 AM Changeset [6885] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Modified help text …
7:57 AM Changeset [6884] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Since the run time …

Nov 23, 2022:

1:37 PM Changeset [6883] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Fixed …

Nov 22, 2022:

3:55 PM Changeset [6882] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added methylation …
1:47 PM Changeset [6881] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Implemented …
11:32 AM Changeset [6880] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Implemented …
8:51 AM Changeset [6879] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Started with the …

Nov 18, 2022:

2:17 PM Changeset [6878] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a flag …
11:19 AM Changeset [6877] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added thumbnails …
11:00 AM Changeset [6876] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a lot of …
8:47 AM Changeset [6875] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Updated the R …

Nov 17, 2022:

9:46 AM Changeset [6874] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard The R script now …
8:51 AM Changeset [6873] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added the R script …

Nov 16, 2022:

2:11 PM Changeset [6872] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a conteiner …
1:44 PM Changeset [6871] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a simple …
8:18 AM Changeset [6870] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a job …

Nov 15, 2022:

1:00 PM Changeset [6869] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a wizard for …
8:49 AM Changeset [6868] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added an item list …
8:47 AM Changeset [6867] by Nicklas Nordborg
References #1419: Methylation beta-analysis wizard Added a new …

Nov 14, 2022:

1:56 PM Ticket #1419 (Methylation beta-analysis wizard) created by Nicklas Nordborg
Implement a wizard that calculate beta-values for methylation …
7:31 AM Changeset [6866] by Nicklas Nordborg
References #1418: Implement support for methylation data Added IDAT

Nov 9, 2022:

7:46 AM Changeset [6865] by Nicklas Nordborg
References #1418: Implement support for methylation data Added …
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