Timeline



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 Nordborg
Switched from illumina2bam_wrapper to picard for demultiplexing. …
8:10 AM Changeset [2429] by Nicklas Nordborg
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 Nordborg
References #547: Start Demux and Merge Export barcode files needed by …
2:43 PM Changeset [2421] by Nicklas Nordborg
Renamed the 'filtered' step to 'masked'. See …
2:41 PM Changeset [2420] by Nicklas Nordborg
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 Nordborg
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 Nordborg
References #593: Start filter and alignment Removed 'filter_' prefix …
1:23 PM Changeset [2413] by Nicklas Nordborg
Remove 'filter_' prefix in the PE_filter script.
9:00 AM Changeset [2412] by Nicklas Nordborg
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 Nordborg
(diff)
8:17 AM net.sf.basedb.reggie/notes215 edited by Nicklas Nordborg
(diff)
8:16 AM net.sf.basedb.reggie edited by Nicklas Nordborg
(diff)
8:14 AM net.sf.basedb.reggie/notes2151 created by Nicklas Nordborg
8:08 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 2.15.1 (diff)
8:06 AM reggie-2.15.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 2.15.1
8:06 AM Ticket #594 (Changes for NextSeq support) closed by Nicklas Nordborg
fixed
8:05 AM Changeset [2411] by Nicklas Nordborg
Tagging Reggie 2.15.1
8:04 AM Changeset [2410] by Nicklas Nordborg
Preparing to release Reggie 2.15.1
8:02 AM Changeset [2409] by Nicklas Nordborg
References #594: Changes for NextSeq? support Hide 'B' position when …

May 8, 2014:

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

May 7, 2014:

12:39 PM Changeset [2406] by Nicklas Nordborg
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 Nordborg
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 Nordborg
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 Nordborg
References #533: Add secondary analysis section to Reggie Change …
1:10 PM Changeset [2399] by Nicklas Nordborg
References #593: Start filter and alignment Running …
11:20 AM Changeset [2398] by Nicklas Nordborg
Adding statistics_tophat.sh
9:02 AM Changeset [2397] by Nicklas Nordborg
References #593: Start filter and alignment Now running tophat and …
8:59 AM Changeset [2396] by Nicklas Nordborg
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 Nordborg
References #593: Start filter and alignment Generate a script that is …
2:36 PM Changeset [2393] by Nicklas Nordborg
Adding PE_filter.sh script. Changes from original script is that …
12:01 PM Ticket #594 (Changes for NextSeq support) created by Nicklas Nordborg
A new NextSeq machine is arriving soon. There are some changes we …

Apr 28, 2014:

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

Apr 25, 2014:

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

Apr 24, 2014:

3:40 PM Changeset [2377] by Nicklas Nordborg
References #547: Start Demux and Merge Added 'debug' option to the wizard.
12:58 PM Changeset [2376] by Nicklas Nordborg
References #533: Add secondary analysis section to Reggie Use 'x' …
12:48 PM Changeset [2375] by Nicklas Nordborg
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 Nordborg
Part of #533. The wizard is started after successfully demultiplexing …
2:23 PM Changeset [2374] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern Fixed for …
12:32 PM Changeset [2373] by Nicklas Nordborg
References #547: Start Demux and Merge Summarize number of …
10:57 AM Changeset [2372] by Nicklas Nordborg
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 Nordborg
fixed: (In [2371]) Fixes #560: Use annotations on Histology work list to …
7:50 AM Changeset [2371] by Nicklas Nordborg
Fixes #560: Use annotations on Histology work list to indicate …

Apr 22, 2014:

2:09 PM Changeset [2370] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern Fixed on the …
9:47 AM Changeset [2369] by Nicklas Nordborg
References #571: Update Reggie to new scripting pattern Fixed on the …

Apr 17, 2014:

12:25 PM Ticket #579 (Store serial number of sequencers as annotations on hardware items) closed by Nicklas Nordborg
fixed: (In [2368]) Fixes #579: Store serial number of sequencers as …
12:24 PM Changeset [2368] by Nicklas Nordborg
Fixes #579: Store serial number of sequencers as annotations on …
11:12 AM Changeset [2367] by Nicklas Nordborg
References #548: Register Demux and Merge as ended Submit …

Apr 16, 2014:

2:52 PM Changeset [2366] by Nicklas Nordborg
References #548: Register Demux and Merge as ended Display number of …
2:51 PM Changeset [2365] by Nicklas Nordborg
References #547: Start Demux and Merge Generated sript for demux now …
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