Timeline


and

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 …

Apr 22, 2014:

2:09 PM Changeset [2370] by nicklas
References #571: Update Reggie to new scripting pattern Fixed on the …
9:47 AM Changeset [2369] by nicklas
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
fixed: (In [2368]) Fixes #579: Store serial number of sequencers as …
12:24 PM Changeset [2368] by nicklas
Fixes #579: Store serial number of sequencers as annotations on …
11:12 AM Changeset [2367] by nicklas
References #548: Register Demux and Merge as ended Submit …

Apr 16, 2014:

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

Apr 15, 2014:

2:41 PM Changeset [2364] by nicklas
References #548: Register Demux and Merge as ended Started with the …

Apr 14, 2014:

2:21 PM Changeset [2363] by nicklas
References #547: Start Demux and Merge Cleaning up a bit.
1:24 PM Changeset [2362] by nicklas
References #547: Start Demux and Merge Added ScriptBuilder for more …
10:32 AM Changeset [2361] by nicklas
References #547: Start Demux and Merge Implemented primitive progress …

Apr 11, 2014:

3:10 PM Changeset [2360] by olle
Refs #592. Outermost Ant build file build.xml and file …
2:39 PM Ticket #592 (Lab environment extension improved report routines) created by olle
The lab environment extension should have improved report routines, …
2:19 PM Ticket #529 (Retrieve and store temperature and humidity measurements) closed by olle
fixed: Ticket closed as a first version of the lab environment extension has …
2:09 PM Milestone LabEnv v1.0 completed
The first release of the LabEnv extension to BASE, a package allowing …
2:02 PM net.sf.basedb.labenv edited by olle
Revision set to 2358 and Date to 2014-04-11 (diff)
1:50 PM Changeset [2359] by nicklas
References #547: Start Demux and Merge Added call to …
1:50 PM labenv-1.0.tar.gz attached to net.sf.basedb.labenv by olle
Exchnaged package labenv-1.0.tar.gz from trunk for package from tags/1.0
12:41 PM Changeset [2358] by olle
Tagging release 1.0
12:33 PM net.sf.basedb.labenv edited by olle
Filesize for labenv-1.0.tar.gz set to 3.9 MB (diff)
12:25 PM PluginDownload edited by olle
Added entry for LabEnv 1.0 extension to table of BASE 3 compatible … (diff)
12:10 PM Changeset [2357] by olle
Refs #529. Configuration file META-INF/extensions.xml updated by …
10:43 AM Changeset [2356] by nicklas
References #547: Start Demux and Merge Create a single job on the …

Apr 10, 2014:

1:47 PM Changeset [2355] by nicklas
Removing branches/ssh-test from Reggie since it is now implemented in …
1:37 PM Changeset [2354] by nicklas
References #529. Add eclipse project and classpath file and svn:ignore …
11:28 AM Changeset [2353] by olle
Refs #529. Lab environment extension updated in text file readme.txt
11:11 AM Changeset [2352] by olle
Refs #529. Lab environment extension updated when exporting …
10:59 AM Ticket #539 (Set "Disable log" flag on some annotation types) closed by nicklas
fixed: (In [2351]) Fixes #539: Set "Disable log" flag on some annotation types
10:59 AM Changeset [2351] by nicklas
Fixes #539: Set "Disable log" flag on some annotation types
10:49 AM Ticket #515 (Store sequence for barcodes as annotations on tags) closed by nicklas
fixed: (In [2350]) Fixes #515: Store sequence for barcodes as annotations on tags
10:49 AM Changeset [2350] by nicklas
Fixes #515: Store sequence for barcodes as annotations on tags
10:33 AM Changeset [2349] by olle
Refs #529. Lab environment extension updated to only output 2 decimals …
10:00 AM Changeset [2348] by nicklas
References #547: Start Demux and Merge FlowCellSampleSheetExporter
9:52 AM Changeset [2347] by olle
Refs #529. Lab environment extension updated in text file README: …
9:38 AM Changeset [2346] by olle
Refs #529. Lab environment extension updated in outermost Ant build …

Apr 9, 2014:

2:56 PM Changeset [2345] by olle
Refs #529. Lab environment extension updated by moving JAR file …
1:25 PM Changeset [2344] by nicklas
Merge 2.15-stable from rev 2261 (2.15-beta-2) to rev 2343 (2.15) back …
1:19 PM Changeset [2343] by nicklas
Remove HiSeqPosition annotation physical bioassay since it should be …
11:49 AM Changeset [2342] by olle
Refs #529. Lab environment extension updated by replacing all …
9:28 AM Changeset [2341] by olle
Refs #529. JSP files labsensorinfo.jsp, …
8:55 AM Milestone Reggie v2.15 completed
Redesign clustering and sequencing startup wizard to better match …
8:54 AM PluginDownload edited by nicklas
Released Reggie 2.15 (diff)
8:53 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.15 (diff)
8:51 AM reggie-2.15.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.15
8:51 AM Changeset [2340] by nicklas
Tagging Reggie 2.15
8:50 AM Changeset [2339] by nicklas
Preparing to release Reggie 2.15
8:34 AM Changeset [2338] by olle
Refs #529. Class/file LabEnvService.java in …
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