Timeline


and

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, …

May 16, 2014:

4:39 PM Changeset [2433] by olle
Refs #592. Lab environment extension updated in servlet to reduce the …
4:31 PM Changeset [2432] by olle
Refs #592. Lab environment extension updated with first version of …
12:31 PM Changeset [2431] by olle
Refs #592. Lab environment extension updated in servlet, in order to …
8:12 AM Changeset [2430] by nicklas
Switched from illumina2bam_wrapper to picard for demultiplexing. …
8:10 AM Changeset [2429] by nicklas
References #547: Start Demux and Merge Switched from …
7:28 AM Changeset [2428] by olle
Refs #592. Lab environment extension updated in header title for …

May 15, 2014:

4:45 PM Changeset [2427] by olle
Refs #592. Lab environment extension updated in layout of alarm table: …
11:30 AM Changeset [2426] by olle
Refs #592. Lab environment extension updated in alarm text layout: …
7:39 AM Changeset [2425] by olle
Refs #592. Lab environment extension updated in alarm infra-structure …

May 14, 2014:

4:38 PM Changeset [2424] by olle
Refs #592. Lab environment extension updated in alarm infra-structure …
8:47 AM Changeset [2423] by olle
Refs #592. Lab environment extension updated in header title for …

May 13, 2014:

3:40 PM Changeset [2422] by nicklas
References #547: Start Demux and Merge Export barcode files needed by …
2:43 PM Changeset [2421] by nicklas
Renamed the 'filtered' step to 'masked'. See …
2:41 PM Changeset [2420] by nicklas
References #533, #547, #548, #593, #595. Renamed FilteredSequences
8:37 AM Changeset [2419] by olle
Refs #592. Lab environment extension updated to check permission to …

May 12, 2014:

3:58 PM Changeset [2418] by olle
Refs #592. Lab environment extension updated to only use a fixed …
8:13 AM Changeset [2417] by nicklas
References #595: Confirm alignment Saved files are attached to the …

May 9, 2014:

3:01 PM Changeset [2416] by olle
Refs #592. Lab environment extension updated in code formatting: 1. …
2:17 PM Changeset [2415] by olle
Refs #592. Lab environment extension updated with lab environment …
1:24 PM Changeset [2414] by nicklas
References #593: Start filter and alignment Removed 'filter_' prefix …
1:23 PM Changeset [2413] by nicklas
Remove 'filter_' prefix in the PE_filter script.
9:00 AM Changeset [2412] by nicklas
Merged Reggie 2.15.1 to trunk.
8:19 AM Milestone Reggie v2.15.1 completed
Bug fixes for Reggie 2.15 and changes for NextSeq support. See …
8:17 AM net.sf.basedb.reggie edited by nicklas
(diff)
8:17 AM net.sf.basedb.reggie/notes215 edited by nicklas
(diff)
8:16 AM net.sf.basedb.reggie edited by nicklas
(diff)
8:14 AM net.sf.basedb.reggie/notes2151 created by nicklas
8:08 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.15.1 (diff)
8:06 AM reggie-2.15.1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.15.1
8:06 AM Ticket #594 (Changes for NextSeq support) closed by nicklas
fixed
8:05 AM Changeset [2411] by nicklas
Tagging Reggie 2.15.1
8:04 AM Changeset [2410] by nicklas
Preparing to release Reggie 2.15.1
8:02 AM Changeset [2409] by nicklas
References #594: Changes for NextSeq? support Hide 'B' position when …

May 8, 2014:

3:49 PM Changeset [2408] by nicklas
References #594: Changes for NextSeq? support * Added 'Lanes/flow …
10:56 AM Changeset [2407] by nicklas
References #595: Confirm alignment Extended the file listing feature …

May 7, 2014:

12:39 PM Changeset [2406] by nicklas
References #595: Confirm alignment Adding a function for listing and …
8:42 AM Changeset [2405] by olle
Refs #592. Lab environment extension updated in class/file …

May 6, 2014:

1:59 PM Changeset [2404] by nicklas
References #595: Confirm alignment First version of the wizard. It …
12:05 PM Changeset [2403] by olle
Refs #592. Lab environment extension updated in class/file …
11:55 AM Changeset [2402] by olle
Refs #592. Lab environment extension updated in field name and help …
11:37 AM Ticket #595 (Confirm alignment) created by nicklas
Confirmation is needed after the filter/alignment step. The normal …
11:09 AM Changeset [2401] by olle
Refs #592. Lab environment extension updated for displaying graphs of …

May 5, 2014:

1:24 PM Changeset [2400] by nicklas
References #533: Add secondary analysis section to Reggie Change …
1:10 PM Changeset [2399] by nicklas
References #593: Start filter and alignment Running …
11:20 AM Changeset [2398] by nicklas
Adding statistics_tophat.sh
9:02 AM Changeset [2397] by nicklas
References #593: Start filter and alignment Now running tophat and …
8:59 AM Changeset [2396] by nicklas
Adding tophat_single.sh and sync_resyltfiles.sh scrips. tophat_single …
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