Timeline


and

Jun 16, 2014:

9:35 AM Changeset [2510] by nicklas
References #533: Add secondary analysis section to Reggie Include …
9:16 AM Changeset [2509] by nicklas
Merge Reggie 2.15.3 to the trunk.
9:01 AM Milestone Reggie v2.15.3 completed
Bug fixes for Reggie 2.15. See [wiki:net.sf.basedb.reggie Reggie …
9:00 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.15.3 (diff)
8:59 AM reggie-2.15.3.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.15.3
8:58 AM Changeset [2508] by nicklas
Tagging Reggie 2.15.3
8:57 AM Changeset [2507] by nicklas
Preparing to release Reggie 2.15.3

Jun 13, 2014:

12:03 PM net.sf.basedb.reggie/notes216 created by nicklas
8:53 AM Changeset [2506] by nicklas
References #604: New wizard "RNA dilution registration" Removed debug …
8:52 AM Ticket #604 (New wizard "RNA dilution registration") closed by nicklas
fixed: (In [2505]) Fixes #604: New wizard "RNA dilution registration" Added …
8:52 AM Changeset [2505] by nicklas
Fixes #604: New wizard "RNA dilution registration" Added the new RNA …
8:12 AM Changeset [2504] by nicklas
References #604: New wizard "RNA dilution registration" The lab …

Jun 12, 2014:

2:51 PM Ticket #603 (Default sequencing cycles for NextSeq should be 76-6-76) closed by nicklas
fixed: (In [2503]) Fixes #603: Default sequencing cycles for NextSeq? should …
2:51 PM Changeset [2503] by nicklas
Fixes #603: Default sequencing cycles for NextSeq? should be 76-6-76
12:44 PM Ticket #606 (Switch to JDOM 2) created by nicklas
The BASE core switched to JDOM 2 in BASE 3.4. The old JDOM 1.1 support …
12:00 PM Changeset [2502] by nicklas
Updating classpath to point to the current JAR files.
11:56 AM Ticket #605 (Switch to JDOM 2) created by nicklas
The BASE core switched to JDOM 2 in BASE 3.4. The old JDOM 1.1 support …
11:31 AM Changeset [2501] by olle
Refs #530. Case summary updated for specific event dates by optional …
11:30 AM Ticket #604 (New wizard "RNA dilution registration") created by nicklas
Due to changed workflow in the lab it would be nice to have a new …

Jun 11, 2014:

4:10 PM Ticket #603 (Default sequencing cycles for NextSeq should be 76-6-76) created by nicklas
The current default values in the "Create flow cells" wizard are …

Jun 10, 2014:

1:17 PM Changeset [2500] by nicklas
References #571: Update Reggie to new scripting pattern Fixed call to …

Jun 5, 2014:

4:06 PM Milestone LabEnv v1.1 completed
An update of the LabEnv extension to BASE, a package allowing storage …
4:04 PM Ticket #592 (Lab environment extension improved report routines) closed by olle
fixed: Ticket closed as a the lab environment extension has been updated with …
3:42 PM Changeset [2499] by nicklas
References #595: Confirm alignment Display PT_READS in the …
3:41 PM Changeset [2498] by nicklas
References #548: Register Demux and Merge as ended Display PT_READS …
3:41 PM Changeset [2497] by nicklas
References #547: Start Demux and Merge Added trimmomatic to the …
3:31 PM labenv-1.1.tar.gz attached to net.sf.basedb.labenv by olle
LabEnv version 1.1 package
3:26 PM Changeset [2496] by nicklas
Adding svn properties
3:24 PM Changeset [2495] by nicklas
Adding wrapper for calling trimmomatic. Includes default settings for …
3:02 PM Changeset [2494] by olle
unwanted
2:55 PM Changeset [2493] by olle
Checking out tagged release LabEnv 1.1
2:48 PM net.sf.basedb.labenv edited by olle
LabEnv info page updated with data for version 1.1. (diff)
2:14 PM PluginDownload edited by nicklas
(diff)
2:14 PM PluginDownload edited by nicklas
Updated note about web service support. (diff)
2:10 PM net.sf.basedb.examples.webservices edited by nicklas
Updated note about web service support. (diff)
2:09 PM Changeset [2492] by olle
LabEnv? tagged release 1.1
1:55 PM Changeset [2491] by olle
Refs #592. Lab environment extension updated by setting version number …
1:43 PM Changeset [2490] by olle
Refs #592. Configuration file META-INF/extensions.xml updated by …
1:32 PM Changeset [2489] by olle
Refs #592. Lab environment extension updated in versions of external …
1:29 PM Ticket #602 (Focus fields on the YubiKey tab) closed by nicklas
fixed: (In [2488]) Fixes #602: Focus fields on the YubiKey? tab
1:29 PM Changeset [2488] by nicklas
Fixes #602: Focus fields on the YubiKey? tab
1:26 PM Ticket #602 (Focus fields on the YubiKey tab) created by nicklas
When switching to the YubiKey tab in the edit user dialog it would be …
1:22 PM Ticket #601 (NullPointerException when trying to assign a YubiKey to a new user) closed by nicklas
fixed: (In [2487]) Fixes #601: NullPointerException? when trying to assign a …
1:22 PM Changeset [2487] by nicklas
Fixes #601: NullPointerException? when trying to assign a YubiKey? to a …
11:21 AM Changeset [2486] by olle
Refs #592. Lab environment extension updated in JSP files by removing …
11:02 AM Ticket #601 (NullPointerException when trying to assign a YubiKey to a new user) created by nicklas
Start creating a new user and then switch to the YubiKey tab. Instead …
8:56 AM Ticket #599 (YubiKey package is missing yubikey-extended-properties.xml) closed by nicklas
fixed: (In [2485]) Fixes #599: YubiKey? package is missing …
8:56 AM Changeset [2485] by nicklas
Fixes #599: YubiKey? package is missing yubikey-extended-properties.xml
8:54 AM Ticket #600 (Installation instructions for YubiKey extensions is not clear) closed by nicklas
fixed
8:54 AM net.sf.basedb.yubikey/install edited by nicklas
Fixes #600 (diff)
8:49 AM Ticket #600 (Installation instructions for YubiKey extensions is not clear) created by nicklas
Step 3: If this is a FIRST-TIME INSTALLATION go through the step …
8:10 AM net.sf.basedb.yubikey/install edited by nicklas
Add note about missing yubikey-extended-properties.xml (diff)
8:07 AM Ticket #599 (YubiKey package is missing yubikey-extended-properties.xml) created by nicklas
Workaround is to download this file from the subversion repository: …

Jun 4, 2014:

12:19 PM PluginDownload edited by nicklas
Updating information about new releases (diff)
12:16 PM Changeset [2484] by nicklas
Preparing for future release YubiKey? 1.1
12:16 PM Milestone YubiKey v1.0 completed
Implementing an authentication module for YubiKey. …
12:15 PM net.sf.basedb.yubikey edited by nicklas
Released YubiKey? 1.0 (diff)
12:08 PM yubikey-1.0.tar.gz attached to net.sf.basedb.yubikey by nicklas
YubiKey? 1.0
12:07 PM Ticket #580 (Authenticate users using YubiKey sticks) closed by nicklas
fixed
12:07 PM Changeset [2483] by nicklas
Tagging YubiKey? 1.0
12:06 PM Changeset [2482] by nicklas
Preparing to release Yubikey 1.0
12:00 PM Changeset [2481] by olle
Refs #592. Lab environment extension updated for displaying lab …
11:45 AM Changeset [2480] by nicklas
Preparing for future release print package 1.2
11:44 AM Milestone Print package v1.1 completed
See Print package extension page for more …
11:43 AM net.sf.basedb.print edited by nicklas
Released print package 1.1 (diff)
11:42 AM base-print-1.1.tar.gz attached to net.sf.basedb.print by nicklas
Print package 1.1
11:42 AM Changeset [2479] by nicklas
Tagging print package 1.1
11:41 AM Changeset [2478] by nicklas
Preparing to release print package 1.1
11:38 AM Changeset [2477] by nicklas
Preparing for future release MeV launcher 1.12
11:34 AM Milestone MeV Launcher 1.11 completed
For more information see the [wiki:net.sf.basedb.mev MEV Launcher …
11:29 AM net.sf.basedb.mev edited by nicklas
Released MeV Launcher 1.11 (diff)
11:26 AM mev-launcher-1.11.tar.gz attached to net.sf.basedb.mev by nicklas
MeV Launcher 1.11
11:26 AM Changeset [2476] by nicklas
Tagging Mev launcher 1.11
11:25 AM Changeset [2475] by nicklas
Preparing to release MEV launvher 1.11
11:21 AM Changeset [2474] by olle
Refs #592. Lab environment extension updated in XML file …
11:20 AM Changeset [2473] by nicklas
Preparing for future release Ftp server 1.4
11:19 AM Milestone FTP Server v1.3 completed
For more information see the [wiki:net.sf.basedb.ftp FTP Server …
11:18 AM net.sf.basedb.ftp edited by nicklas
Released Ftp server 1.3 (diff)
11:17 AM base-ftpserver-1.3.tar.gz attached to net.sf.basedb.ftp by nicklas
BASE FTP Server Extension 1.3
11:16 AM Changeset [2472] by nicklas
Tagging Ftp server 1.3
11:15 AM Changeset [2471] by nicklas
Preparing to release Ftp server 1.3
11:13 AM Changeset [2470] by nicklas
Preparing for future release example code 1.7
11:12 AM Milestone Example code v1.6 completed
For more information see [wiki:net.sf.basedb.examplecode Example code …
11:11 AM net.sf.basedb.examplecode edited by nicklas
Released exemple code 1.6 (diff)
11:09 AM base-examples-1.6.tar.gz attached to net.sf.basedb.examplecode by nicklas
Example code 1.6
10:03 AM Changeset [2469] by nicklas
Tagging example code 1.6
10:01 AM Changeset [2468] by nicklas
Preparing to release example code 1.6

Jun 3, 2014:

8:22 AM Changeset [2467] by olle
Refs #592. Lab environment extension updated for displaying lab …

Jun 2, 2014:

4:16 PM Changeset [2466] by olle
Refs #592. Lab environment extension updated to report an alarm for …
1:04 PM Changeset [2465] by olle
Refs #592. Lab environment extension updated for weekly and overview …
10:02 AM Changeset [2464] by nicklas
References #547: Start Demux and Merge Do not set TILE_LIMIT for …
9:59 AM Changeset [2463] by olle
Refs #592. Lab environment extension updated to support display of lab …

May 28, 2014:

7:24 AM Changeset [2462] by olle
Refs #592. Lab environment extension updated with a copy of the Reggie …

May 26, 2014:

1:41 PM Ticket #598 (Pooling wizard can't show flag and warning at the same time) closed by nicklas
fixed: (In [2461]) Fixes #598: Pooling wizard can't show flag and warning at …
1:41 PM Changeset [2461] by nicklas
Fixes #598: Pooling wizard can't show flag and warning at the same …
1:09 PM Ticket #598 (Pooling wizard can't show flag and warning at the same time) created by nicklas
Libraries that get a warning due to low concentration or high adapter …
9:32 AM Changeset [2460] by nicklas
References #593: Start masking and alignment Improved error handling …
9:08 AM Changeset [2459] by nicklas
References #548: Register Demux and Merge as ended Exit script if the …

May 23, 2014:

1:44 PM Changeset [2458] by nicklas
References #548: Register Demux and Merge as ended Display failed …
1:21 PM Changeset [2457] by nicklas
References #547: Start Demux and Merge Get rid of problematic …
1:11 PM Changeset [2456] by nicklas
References #547: Start Demux and Merge Trim whitespace values from …
1:08 PM Changeset [2455] by nicklas
References #547: Start Demux and Merge Avoid 'find' command to choke …
11:28 AM Changeset [2454] by nicklas
Merging Reggie 2.15.2 to the trunk.
10:56 AM Milestone Reggie v2.15.2 completed
Adapter peak information in library registration and pooling wizards. …
10:54 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.15.2 (diff)
10:53 AM reggie-2.15.2.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.15.2
10:53 AM Changeset [2453] by nicklas
Tagging Reggie 2.15.2
10:52 AM Changeset [2452] by nicklas
Preparing to release Reggie 2.15.2
10:50 AM net.sf.basedb.reggie/notes2152 created by nicklas
Adding updated notes for Reggie 2.15.2
10:44 AM Ticket #596 (Import adapter peak information when registering libraries) closed by nicklas
fixed
10:44 AM Ticket #597 (Display adapter peak fraction in the pooling wizard) closed by nicklas
fixed
9:54 AM Changeset [2451] by nicklas
References #597: Display adapter peak fraction in the pooling wizard …
9:43 AM Changeset [2450] by nicklas
References #597: Display adapter peak fraction in the pooling wizard …

May 22, 2014:

4:05 PM Changeset [2449] by nicklas
References #596: Import adapter peak information when registering …
2:08 PM Changeset [2448] by nicklas
References #596: Import adapter peak information when registering …
12:59 PM Changeset [2447] by nicklas
References #596: Import adapter peak information when registering …
12:34 PM Changeset [2446] by nicklas
References #547: Start Demux and Merge Adding 'rm <tmp-folder>' back …
12:31 PM Ticket #597 (Display adapter peak fraction in the pooling wizard) created by nicklas
This is related to #596. The pooling wizard should display the …
12:00 PM Ticket #596 (Import adapter peak information when registering libraries) created by nicklas
The library registration wizard currently import values for the …
11:36 AM Changeset [2445] by nicklas
References #547: Start Demux and Merge Use 'getFile' instead of …
10:29 AM Changeset [2444] by olle
Refs #592. Lab environment extension updated to hopefully make e-mail …
10:27 AM Changeset [2443] by nicklas
References #547: Start Demux and Merge Generate .gz compressed files …
8:48 AM Changeset [2442] by nicklas
Check enironment variable PicardMemory? for amount of memory to give to …

May 20, 2014:

11:43 AM Changeset [2441] by nicklas
References #547: Start Demux and Merge * Do not start multiple demux …

May 19, 2014:

3:37 PM Changeset [2440] by olle
Refs #592. Lab environment extension updated by associating main "Lab …
1:45 PM Changeset [2439] by olle
Refs #592. Lab environment extension updated in JSP files to have more …
1:15 PM Changeset [2438] by nicklas
References #548: Register Demux and Merge as ended Remove job folder …
12:55 PM Changeset [2437] by nicklas
References #548: Register Demux and Merge as ended Display demux …
11:00 AM Changeset [2436] by nicklas
References #547: Start Demux and Merge Do not skip last base in …
10:54 AM Changeset [2435] by nicklas
References #547: Start Demux and Merge Saving demultiplex_metrics …
9:11 AM Changeset [2434] by nicklas
References #547: Start Demux and Merge Adding PF_NNNN_PCT, …
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