Timeline



Sep 13, 2023:

2:01 PM Ticket #1522 (Add support for setting more options for submitting jobs to the cluster) updated by Nicklas Nordborg
In 7348: […]
2:01 PM Changeset [7348] by Nicklas Nordborg
References #1522: Add support for setting more options for submitting …
1:53 PM Ticket #1523 (Remove the example configuration for the old OpenGrid cluster from ...) closed by Nicklas Nordborg
fixed: In 7347: […]
1:53 PM Changeset [7347] by Nicklas Nordborg
Fixes #1523: Remove the example configuration for the old OpenGrid
12:01 PM Ticket #1523 (Remove the example configuration for the old OpenGrid cluster from ...) created by Nicklas Nordborg
We have been using the new Slurm cluster a long time now, and the old …
11:59 AM Ticket #1522 (Add support for setting more options for submitting jobs to the cluster) updated by Nicklas Nordborg
In 7346: […]
11:59 AM Changeset [7346] by Nicklas Nordborg
References #1522: Add support for setting more options for submitting …
9:10 AM Ticket #1522 (Add support for setting more options for submitting jobs to the cluster) created by Nicklas Nordborg
When submitting jobs to the cluster we need to specify some options …

Sep 11, 2023:

1:47 PM Changeset [7345] by Nicklas Nordborg
Merge Reggie 4.49.2 to the trunk.
1:45 PM Milestone Reggie v4.49.2 completed
Bug fixes and enhancements for Reggie 4.49.1. Revision Log: …
1:45 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49.2 (diff)
1:44 PM reggie-4.49.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.49.2
1:39 PM Changeset [7344] by Nicklas Nordborg
Tagging Reggie 4.49.2
1:38 PM Changeset [7343] by Nicklas Nordborg
Preparing to release Reggie 4.49.2
1:37 PM Ticket #1521 (The Secondary analysis cleanup wizard need to support more item types) closed by Nicklas Nordborg
fixed: In 7342: […]
1:37 PM Changeset [7342] by Nicklas Nordborg
Fixes #1521: The Secondary analysis cleanup wizard need to support …
12:01 PM Ticket #1521 (The Secondary analysis cleanup wizard need to support more item types) created by Nicklas Nordborg
It currently has support for * DemuxedSequences * …
11:35 AM Changeset [7341] by Nicklas Nordborg
Merge Reggie 4.49.1 to the trunk
11:31 AM Milestone Reggie v4.49.1 completed
Bug fixes and enhancements for Reggie 4.49. Revision Log: …
11:31 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49.1 (diff)
11:29 AM reggie-4.49.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.49.1
11:28 AM Changeset [7340] by Nicklas Nordborg
Tagging Reggie 4.49.1
11:27 AM Changeset [7339] by Nicklas Nordborg
Preparing to release Reggie 4.49.1
9:55 AM Tickets #1515,​1519,​1520 batch updated by Nicklas Nordborg
fixed
9:12 AM Ticket #1520 (Output a file with values used in the allelic imbalance test) updated by Nicklas Nordborg
In 7338: […]
9:12 AM Changeset [7338] by Nicklas Nordborg
References #1520: Output a file with values used in the allelic …
7:56 AM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7337: […]
7:56 AM Changeset [7337] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …

Sep 8, 2023:

1:47 PM Ticket #1520 (Output a file with values used in the allelic imbalance test) updated by Nicklas Nordborg
In 7336: […]
1:47 PM Changeset [7336] by Nicklas Nordborg
References #1520: Output a file with values used in the allelic …
1:01 PM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7335: […]
1:01 PM Changeset [7335] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …
11:14 AM Ticket #1520 (Output a file with values used in the allelic imbalance test) created by Nicklas Nordborg
Since it takes a while to test different values for the tau
11:11 AM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7334: […]
11:10 AM Changeset [7334] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …

Sep 7, 2023:

1:52 PM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7333: […]
1:52 PM Changeset [7333] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …
1:50 PM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7332: […]
1:50 PM Changeset [7332] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …
1:40 PM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) updated by Nicklas Nordborg
In 7331: […]
1:40 PM Changeset [7331] by Nicklas Nordborg
References #1519: Add support for using "bimodality_coefficient" as a …

Sep 6, 2023:

6:51 AM Ticket #1519 (Add support for using "bimodality_coefficient" as a test for allelic ...) created by Nicklas Nordborg
The bimodality_coefficient() is part of the mousetrap R package, …

Sep 4, 2023:

2:56 PM Ticket #1517 (Add support for setting the "minCounts" parameter in the call to ...) closed by Nicklas Nordborg
fixed: In 7330: […]
2:56 PM Changeset [7330] by Nicklas Nordborg
Fixes #1517: Add support for setting the "minCounts" parameter in the …
2:54 PM Ticket #1518 (Submitting multiple types of jobs as a single batch) closed by Nicklas Nordborg
fixed: In 7329: […]
2:54 PM Changeset [7329] by Nicklas Nordborg
Fixes #1518: Submitting multiple types of jobs as a single batch
11:26 AM Ticket #1518 (Submitting multiple types of jobs as a single batch) created by Nicklas Nordborg
After the demux (or FASTQ import) multiple jobs are started by the …
11:16 AM Ticket #1517 (Add support for setting the "minCounts" parameter in the call to ...) created by Nicklas Nordborg
This is similar to #1516.
9:08 AM Ticket #1516 (Add support for setting the "penalty" parameter in the call to ...) closed by Nicklas Nordborg
fixed: In 7328: […]
9:08 AM Changeset [7328] by Nicklas Nordborg
Fixes #1516: Add support for setting the "penalty" parameter in the …
7:43 AM Ticket #1516 (Add support for setting the "penalty" parameter in the call to ...) created by Nicklas Nordborg
We noticed that there were some samples that wasn't segmented in …

Sep 1, 2023:

11:29 AM Ticket #1515 (Pick up the "Non-aberrant" flag from ASCAT result and import as an ...) updated by Nicklas Nordborg
In 7327: […]
11:29 AM Changeset [7327] by Nicklas Nordborg
References #1515: Pick up the "Non-aberrant" flag from ASCAT result …

Aug 31, 2023:

8:38 PM Ticket #1515 (Pick up the "Non-aberrant" flag from ASCAT result and import as an ...) updated by Nicklas Nordborg
In 7326: […]
8:38 PM Changeset [7326] by Nicklas Nordborg
References #1515: Pick up the "Non-aberrant" flag from ASCAT result …
7:29 PM Ticket #1515 (Pick up the "Non-aberrant" flag from ASCAT result and import as an ...) updated by Nicklas Nordborg
In 7325: […]
7:29 PM Changeset [7325] by Nicklas Nordborg
References #1515: Pick up the "Non-aberrant" flag from ASCAT result …
7:11 PM Ticket #1515 (Pick up the "Non-aberrant" flag from ASCAT result and import as an ...) updated by Nicklas Nordborg
In 7324: […]
7:11 PM Changeset [7324] by Nicklas Nordborg
References #1515: Pick up the "Non-aberrant" flag from ASCAT result …
6:47 PM Ticket #1515 (Pick up the "Non-aberrant" flag from ASCAT result and import as an ...) created by Nicklas Nordborg
2:05 PM Ticket #1512 (Limit the number of threads used by allelecounter) updated by Nicklas Nordborg
In 7323: […]
2:05 PM Changeset [7323] by Nicklas Nordborg
References #1512: Limit the number of threads used by allelecounter …
9:27 AM Ticket #1514 (Display information about parent alignments in the ASCAT confirmation ...) closed by Nicklas Nordborg
fixed: In 7322: […]
9:27 AM Changeset [7322] by Nicklas Nordborg
Fixes #1514: Display information about parent alignments in the ASCAT …

Aug 30, 2023:

2:58 PM Ticket #1514 (Display information about parent alignments in the ASCAT confirmation ...) created by Nicklas Nordborg
It would be useful to have the number of aligned reads, coverage and …
2:56 PM Ticket #1513 (Add link to the case summary in the ASCAT confirmation wizard) closed by Nicklas Nordborg
fixed: In 7321: […]
2:56 PM Changeset [7321] by Nicklas Nordborg
Fixes #1513: Add link to the case summary in the ASCAT confirmation wizard
2:56 PM Ticket #1513 (Add link to the case summary in the ASCAT confirmation wizard) created by Nicklas Nordborg
2:40 PM Ticket #1512 (Limit the number of threads used by allelecounter) closed by Nicklas Nordborg
fixed: In 7320: […]
2:40 PM Changeset [7320] by Nicklas Nordborg
Fixes #1512: Limit the number of threads used by allelecounter We now …
2:39 PM Ticket #1512 (Limit the number of threads used by allelecounter) created by Nicklas Nordborg
The default settings for the ASCAT analysis is to use 8 cores since …
2:34 PM Ticket #1511 (Increase the delay between ASCAT jobs) closed by Nicklas Nordborg
fixed: In 7319: […]
2:34 PM Changeset [7319] by Nicklas Nordborg
Fixes #1511: Increase the delay between ASCAT jobs Increased the …
9:14 AM Ticket #1511 (Increase the delay between ASCAT jobs) created by Nicklas Nordborg
When submitting multiple jobs to the cluster there is a default delay …
9:07 AM Changeset [7318] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.49

Aug 29, 2023:

11:13 AM Changeset [7317] by Nicklas Nordborg
Changes for future release Reggie 4.50
11:12 AM Milestone Reggie v4.49 completed
See Reggie extension page for more information.
11:11 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.49 (diff)
11:10 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49 (diff)
11:08 AM reggie-4.49.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.49
11:08 AM Ticket #1500 (Implement ASCAT analysis for WGS data) closed by Nicklas Nordborg
fixed
11:06 AM Changeset [7316] by Nicklas Nordborg
Tagging Reggie 4.49
11:05 AM Changeset [7315] by Nicklas Nordborg
Preparing to release Reggie 4.49
9:58 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7314: […]
9:58 AM Changeset [7314] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Do not …
9:23 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7313: […]
9:23 AM Changeset [7313] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Modified the …
9:08 AM Ticket #1510 (Add a "View file" action to the remote file browser used in several of ...) closed by Nicklas Nordborg
fixed: In 7312: […]
9:08 AM Changeset [7312] by Nicklas Nordborg
Fixes #1510: Add a "View file" action to the remote file browser used …
8:31 AM Ticket #1510 (Add a "View file" action to the remote file browser used in several of ...) created by Nicklas Nordborg
This dialog can currently download the files, and since #1476 also …

Aug 28, 2023:

11:45 AM Changeset [7311] by Nicklas Nordborg
Changes for future release External files support 1.8
11:43 AM Milestone External files support 1.7 completed
An extension package containing support for additional protocols to …
11:43 AM PluginDownload edited by Nicklas Nordborg
Released External files support 1.7 (diff)
11:42 AM net.sf.basedb.xfiles edited by Nicklas Nordborg
Released External files support 1.7 (diff)
11:40 AM xfiles-1.7.tar.gz attached to net.sf.basedb.xfiles by Nicklas Nordborg
External files support 1.7
11:39 AM Changeset [7310] by Nicklas Nordborg
Tagging External files support 1.7
11:39 AM Changeset [7309] by Nicklas Nordborg
Preparing to release External files support 1.7
11:37 AM Ticket #1505 (Add new sections for DNA demuxed and aligned items in the case summary) closed by Nicklas Nordborg
fixed: In 7308: […]
11:37 AM Changeset [7308] by Nicklas Nordborg
Fixes #1505: Add new sections for DNA demuxed and aligned items in the …
11:25 AM net.sf.basedb.varsearch/using edited by Nicklas Nordborg
Clarification about chromosome names (diff)
11:23 AM Changeset [7307] by Nicklas Nordborg
Changes for future release Variant Search 1.10
11:22 AM PluginDownload edited by Nicklas Nordborg
Released Variant Search 1.9 (diff)
11:18 AM Tickets #1508,​1509 batch updated by Nicklas Nordborg
Milestone changed
Milestone renamed
11:18 AM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.9 (diff)
11:17 AM Milestone Variant Search v1.9 completed
See Variant Search extension page for …
11:16 AM varsearch-1.9.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.9
11:14 AM Changeset [7306] by Nicklas Nordborg
Tagging Variant Search 1.9
11:14 AM Changeset [7305] by Nicklas Nordborg
Preparing to release Variant search 1.9
9:52 AM Ticket #1509 (Improve searching for variants on chrM) closed by Nicklas Nordborg
fixed: In 7304: […]
9:52 AM Changeset [7304] by Nicklas Nordborg
Fixes #1509: Improve searching for variants on chrM It is now …
9:05 AM Ticket #1509 (Improve searching for variants on chrM) created by Nicklas Nordborg
Normally when searching for variants on a specific chromosome it is …
9:00 AM Ticket #1508 (Use Apache Commons Compress instead of builtin GZIPInputStream) closed by Nicklas Nordborg
fixed: In 7303: […]
9:00 AM Changeset [7303] by Nicklas Nordborg
Fixes #1508: Use Apache Commons Compress instead of builtin …
8:47 AM Ticket #1508 (Use Apache Commons Compress instead of builtin GZIPInputStream) updated by Nicklas Nordborg
In 7302: […]
8:47 AM Changeset [7302] by Nicklas Nordborg
References #1508: Use Apache Commons Compress instead of builtin …

Aug 25, 2023:

2:35 PM Ticket #1508 (Use Apache Commons Compress instead of builtin GZIPInputStream) created by Nicklas Nordborg
One of our servers is running with Java 11 (OpenJDK Runtime …
12:55 PM Ticket #1507 (Load metadata for files when opening the input stream) closed by Nicklas Nordborg
fixed: In 7301: […]
12:55 PM Changeset [7301] by Nicklas Nordborg
Fixes #1507: Load metadata for files when opening the input stream
11:59 AM Ticket #1506 (Update to SSHj 0.35) closed by Nicklas Nordborg
fixed: In 7300: […]
11:59 AM Changeset [7300] by Nicklas Nordborg
Fixes #1506: Update to SSHj 0.35
11:50 AM Ticket #1507 (Load metadata for files when opening the input stream) created by Nicklas Nordborg
When BASE is opening a file for download in the …
11:45 AM Ticket #1506 (Update to SSHj 0.35) created by Nicklas Nordborg

Aug 24, 2023:

8:34 AM Ticket #1505 (Add new sections for DNA demuxed and aligned items in the case summary) created by Nicklas Nordborg
The DNA and RNA demuxed items and alignments are currently displayed …
8:31 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7299: […]
8:31 AM Changeset [7299] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added a small …
8:30 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7298: […]
8:30 AM Changeset [7298] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added …

Aug 23, 2023:

3:35 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7297: […]
3:35 PM Changeset [7297] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Minor …
3:34 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7296: […]
3:34 PM Changeset [7296] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added ASCAT …
1:35 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7295: […]
1:35 PM Changeset [7295] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Use preset …
11:20 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7294: […]
11:20 AM Changeset [7294] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Tumor …

Aug 22, 2023:

4:08 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7293: […]
4:08 PM Changeset [7293] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Started to …

Aug 21, 2023:

12:02 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7292: […]
12:02 PM Changeset [7292] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added a …
11:30 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7291: […]
11:30 AM Changeset [7291] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added the …

Aug 18, 2023:

1:33 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7290: […]
1:33 PM Changeset [7290] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Disabled the …
9:13 AM net.sf.basedb.inca edited by Nicklas Nordborg
Added ZIP file (diff)
9:12 AM IncaXml2Csv-1.3.zip attached to net.sf.basedb.inca by Nicklas Nordborg
IncaXml2Csv 1.3 (zip)
8:39 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7289: […]
8:39 AM Changeset [7289] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Started to …

Aug 16, 2023:

9:54 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7288: […]
9:54 AM Changeset [7288] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Added the …

Aug 15, 2023:

1:41 PM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7287: […]
1:41 PM Changeset [7287] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Implemented …
9:53 AM Changeset [7286] by Nicklas Nordborg
Merge Reggie 4.48.5 to the trunk
9:50 AM Milestone Reggie v4.48.5 completed
Bug fixes and enhancements for Reggie 4.48.4. Revision Log: …
9:49 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.48.5 (diff)
9:48 AM reggie-4.48.5.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.48.5
9:46 AM Changeset [7285] by Nicklas Nordborg
Tagging Reggie 4.48.5
9:46 AM Changeset [7284] by Nicklas Nordborg
Preparing to release Reggie 4.48.5
9:44 AM Ticket #1504 (Allow longer PAD values in JSON files) closed by Nicklas Nordborg
fixed: In 7283: […]
9:44 AM Changeset [7283] by Nicklas Nordborg
Fixes #1504: Allow longer PAD values in JSON files Changed the PAD …
9:05 AM Ticket #1503 (Missing results in the Genotype QC wizard) closed by Nicklas Nordborg
fixed: In 7282: […]
9:05 AM Changeset [7282] by Nicklas Nordborg
Fixes #1503: Missing results in the Genotype QC wizard
9:01 AM Ticket #1504 (Allow longer PAD values in JSON files) created by Nicklas Nordborg
The PAD values is currently limited to 20 characters. There are cases …
8:55 AM Ticket #1503 (Missing results in the Genotype QC wizard) created by Nicklas Nordborg
When running the Genotype QC wizard the results for some alignments …

Aug 14, 2023:

8:53 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7281: […]
8:53 AM Changeset [7281] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Rename result …
8:53 AM Ticket #1500 (Implement ASCAT analysis for WGS data) updated by Nicklas Nordborg
In 7280: […]
8:53 AM Changeset [7280] by Nicklas Nordborg
References #1500: Implement ASCAT analysis for WGS data Generate a …
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