Timeline


and

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 …

Apr 29, 2014:

3:58 PM Changeset [2395] by olle
Refs #592. LabEnv extension updated with weekday and daytime filter …
2:48 PM Changeset [2394] by nicklas
References #593: Start filter and alignment Generate a script that is …
2:36 PM Changeset [2393] by nicklas
Adding PE_filter.sh script. Changes from original script is that …
12:01 PM Ticket #594 (Changes for NextSeq support) created by nicklas
A new NextSeq machine is arriving soon. There are some changes we …

Apr 28, 2014:

3:34 PM Changeset [2392] by nicklas
References #533: Add secondary analysis section to Reggie Added …
2:37 PM Changeset [2391] by nicklas
References #547: Start Demux and Merge Disable all form controls in …
2:36 PM Changeset [2390] by nicklas
References #533: Add secondary analysis section to Reggie Use the …
2:27 PM Changeset [2389] by nicklas
References #593: Start filter and alignment Added 'job priority' and …
8:43 AM Changeset [2388] by nicklas
References #547: Start Demux and Merge Storing FASTQ folder as …

Apr 25, 2014:

1:59 PM Changeset [2387] by nicklas
Scripts used for the demux and merge steps in reggie.
1:47 PM Changeset [2386] by nicklas
References #547: Start Demux and Merge Added project name parameter …
11:56 AM Changeset [2385] by nicklas
References #547: Start Demux and Merge Debug option is automatically …
11:50 AM Changeset [2384] by nicklas
References #547: Start Demux and Merge For now, always use tmp folder …
10:56 AM Changeset [2383] by nicklas
Creating trunk and tags folder for the pipeline project.
10:55 AM Changeset [2382] by nicklas
Creating root folder for the 'pipeline' scripts.
10:55 AM Changeset [2381] by nicklas
Adding folder for other projects.
10:54 AM Changeset [2380] by nicklas
Created in the wrong location
10:54 AM Changeset [2379] by nicklas
Adding folder for other projects.
10:52 AM Changeset [2378] by nicklas
References #547: Start Demux and Merge Added 'priority' option to the …

Apr 24, 2014:

3:40 PM Changeset [2377] by nicklas
References #547: Start Demux and Merge Added 'debug' option to the wizard.
12:58 PM Changeset [2376] by nicklas
References #533: Add secondary analysis section to Reggie Use 'x' …
12:48 PM Changeset [2375] by nicklas
References #593: Start filter and alignment Started to implement this …

Apr 23, 2014:

3:39 PM Ticket #593 (Start masking and alignment) created by nicklas
Part of #533. The wizard is started after successfully demultiplexing …
2:23 PM Changeset [2374] by nicklas
References #571: Update Reggie to new scripting pattern Fixed for …
12:32 PM Changeset [2373] by nicklas
References #547: Start Demux and Merge Summarize number of …
10:57 AM Changeset [2372] by nicklas
References #547: Start Demux and Merge Better error handling when …
7:50 AM Ticket #560 (Use annotations on Histology work list to indicate progress) closed by nicklas
fixed: (In [2371]) Fixes #560: Use annotations on Histology work list to …
7:50 AM Changeset [2371] by nicklas
Fixes #560: Use annotations on Histology work list to indicate …
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