Timeline


and

Oct 23, 2014:

11:24 AM Changeset [2858] by nicklas
Changes for future Reggie 2.18
11:23 AM Changeset [2857] by nicklas
Creating 2.17-stable branch for final 2.17 development.
11:18 AM Changeset [2856] by nicklas
References #641: Import data from cufflinks result files …
11:17 AM Ticket #677 (ant 'clean' should delete downloaded BASE JAR files) closed by nicklas
fixed: (In [2855]) Fixes #677: ant 'clean' should delete downloaded BASE JAR …
11:17 AM Changeset [2855] by nicklas
Fixes #677: ant 'clean' should delete downloaded BASE JAR files
11:03 AM net.sf.basedb.reggie edited by nicklas
(diff)
11:01 AM net.sf.basedb.reggie/HistoryOfReggie edited by nicklas
Add release dates (diff)
10:03 AM reggie-2.16.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.15.3.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.14.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.13.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.12.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.11.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.10.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.9.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.7.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:03 AM reggie-2.6.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:02 AM reggie-2.5.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:02 AM reggie-2.4.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:02 AM reggie-2.2.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:02 AM reggie-2.1.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
10:02 AM net.sf.basedb.reggie/HistoryOfReggie edited by nicklas
(diff)
9:54 AM reggie-2.0.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
9:54 AM reggie-1.6.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
9:54 AM reggie-1.3.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
9:54 AM reggie-1.2.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
9:54 AM reggie-1.0.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
9:53 AM net.sf.basedb.reggie/HistoryOfReggie created by nicklas
8:40 AM net.sf.basedb.reggie/notes217 created by nicklas
8:29 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.17-beta-1 (diff)
8:28 AM reggie-2.17-beta-1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.17-beta-1
8:26 AM Ticket #677 (ant 'clean' should delete downloaded BASE JAR files) created by nicklas
A common problem is that when Reggie moves on to depend on a newer …
8:22 AM Changeset [2854] by nicklas
Tagging Reggie 2.17-beta-1
8:20 AM Changeset [2853] by nicklas
Preparing to release Reggie 2.17-beta-1

Oct 22, 2014:

6:56 PM Changeset [2852] by nicklas
Ignore .project file from Eclipse.
4:02 PM Ticket #676 (Switch to AGPL v3 license) created by nicklas
The PDF generating library (http://www.itextpdf.com/) that we plan to …
12:31 PM Changeset [2851] by nicklas
References #641: Import data from cufflinks result files chromosome …
9:20 AM Changeset [2850] by nicklas
References #630 (and #675): Start cufflinks Adding support for just …
8:51 AM Changeset [2849] by nicklas
References #675: Running a mask/align job as debug for a non-debug …
8:47 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) closed by nicklas
fixed: (In [2848]) Fixes #675: Running a mask/align job as debug for a …
8:47 AM Changeset [2848] by nicklas
Fixes #675: Running a mask/align job as debug for a non-debug demux …
8:05 AM Ticket #675 (Running a mask/align job as debug for a non-debug demux doesn't change ...) created by nicklas
The help text for the debug option says: When running in debug …
8:01 AM Changeset [2847] by nicklas
References #630: Start cufflinks Re-organized configuration parameter …

Oct 21, 2014:

2:21 PM Ticket #674 (Generate document with report of sequencing results) created by nicklas
When the secondary analysis pipeline has been completed we should have …
2:16 PM Ticket #673 (Register RNA QC results from BioAnalyzer runs) created by nicklas
The "Create aliquots on BioAnalyzer/Caliper plates" wizard have …
2:11 PM Ticket #672 (RNA concentration normalization wizard) created by nicklas
A new step that is performed immediately after RNA extraction and …
1:43 PM Changeset [2846] by nicklas
Oh, that's just my pet snake, Reggie!
1:35 PM Changeset [2845] by nicklas
References #526: Retraction wizard Remove unused imports.
1:33 PM Changeset [2844] by nicklas
Oh, that's just my pet snake, Reggie!
8:07 AM Ticket #671 (Save reggie version with jobs) closed by nicklas
fixed: (In [2843]) Fixes #671: Save reggie version with jobs
8:07 AM Changeset [2843] by nicklas
Fixes #671: Save reggie version with jobs
7:58 AM Ticket #671 (Save reggie version with jobs) created by nicklas
Will be possible in BASE 3.3.2 http://base.thep.lu.se/ticket/1871

Oct 20, 2014:

4:00 PM Changeset [2842] by nicklas
References #640: Finalize update to new scripting pattern Found a few …
3:55 PM Changeset [2841] by olle
Refs 526. Servlet class/file RetractionFormServlet.java in …
3:41 PM Ticket #650 (New type of specimen core biopsy) closed by nicklas
fixed: (In [2840]) Fixes #650: New type of specimen core biopsy
3:41 PM Changeset [2840] by nicklas
Fixes #650: New type of specimen core biopsy
2:25 PM Changeset [2839] by olle
Refs #526. First version of the retraction wizard, that lists data for …
1:47 PM Ticket #651 (Add 1x16 pool schema to create mRNA plate wizard) closed by nicklas
fixed: (In [2838]) Fixes #651: Add 1x16 pool schema to create mRNA plate wizard
1:47 PM Changeset [2838] by nicklas
Fixes #651: Add 1x16 pool schema to create mRNA plate wizard
1:34 PM Ticket #638 (Fix issues with not filling all pools on a a plate) closed by nicklas
fixed: (In [2837]) Fixes #638: Fix issues with not filling all pools on a a plate
1:34 PM Changeset [2837] by nicklas
Fixes #638: Fix issues with not filling all pools on a a plate
11:21 AM Ticket #669 (RNAQC Caliper well table import wizard should check if values are missing) closed by nicklas
fixed: (In [2836]) Fixes #669: RNAQC Caliper well table import wizard should …
11:21 AM Changeset [2836] by nicklas
Fixes #669: RNAQC Caliper well table import wizard should check if …
10:44 AM Ticket #670 (Echo commands used for tophat, etc to *.out files) closed by nicklas
fixed: (In [2835]) Fixes #670: Echo commands used for tophat, etc to *.out files
10:44 AM Changeset [2835] by nicklas
Fixes #670: Echo commands used for tophat, etc to *.out files
9:36 AM Ticket #670 (Echo commands used for tophat, etc to *.out files) created by nicklas
Eg: […]
9:28 AM Ticket #640 (Finalize update to new scripting pattern) closed by nicklas
fixed
9:26 AM Changeset [2834] by nicklas
References #640: Finalize update to new scripting pattern Setting …
9:19 AM Changeset [2833] by nicklas
References #640: Finalize update to new scripting pattern Removing …
9:16 AM Changeset [2832] by nicklas
References #640: Finalize update to new scripting pattern Updated the …

Oct 17, 2014:

1:57 PM Ticket #669 (RNAQC Caliper well table import wizard should check if values are missing) created by nicklas
The well table file from caliper is supposed to contain RQS values for …
11:43 AM Changeset [2831] by jari
New version from Christian. added proper argument/option handling; …
11:37 AM Changeset [2830] by jari
Print integers as integers.
9:34 AM Changeset [2829] by nicklas
References #640: Finalize update to new scripting pattern Updated the …

Oct 16, 2014:

3:43 PM Changeset [2828] by nicklas
References #642: Confirm feature extraction as completed New file …
3:40 PM Ticket #668 (Cache result of queries used to count items on Reggie index page) closed by nicklas
fixed: (In [2827]) Fixes #668: Cache result of queries used to count items on …
3:40 PM Changeset [2827] by nicklas
Fixes #668: Cache result of queries used to count items on Reggie …
2:56 PM Changeset [2826] by nicklas
References #642: Confirm feature extraction as completed Started with …
1:45 PM Ticket #668 (Cache result of queries used to count items on Reggie index page) created by nicklas
Some of the (oldest) queries do this, but as new wizards has been …
12:41 PM Changeset [2825] by nicklas
Merge Reggie 2.16.3 to the trunk.
12:39 PM Changeset [2824] by nicklas
Preparing for future release Reggie 2.16.4
12:37 PM Milestone Reggie v2.16.3 completed
Bug fixes for Reggie 2.16.2. See [wiki:net.sf.basedb.reggie Reggie …
12:36 PM PluginDownload edited by nicklas
Released Reggie 2.16.3 (diff)
12:36 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16.3 (diff)
12:35 PM reggie-2.16.3.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16.3
12:34 PM Changeset [2823] by nicklas
Tagging Reggie 2.16.3
12:33 PM Changeset [2822] by nicklas
Preparing to release Reggie 2.16.3
11:58 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) closed by nicklas
fixed: (In [2821]) Fixes #667: Library registration wizard complains about …
11:58 AM Changeset [2821] by nicklas
Fixes #667: Library registration wizard complains about missing …
11:12 AM Changeset [2820] by nicklas
References #667: Library registration wizard complains about missing …
10:55 AM Ticket #667 (Library registration wizard complains about missing concentration for ...) created by nicklas
The qubit and caliper files seems to be ok, but the library …
9:50 AM Changeset [2819] by nicklas
Merge Reggie 2.16.2 to the trunk.
9:46 AM Changeset [2818] by nicklas
Preparing for future release Reggie 2.16.3
9:45 AM Milestone Reggie v2.16.2 completed
Bug fixes for Reggie 2.16.1. See [wiki:net.sf.basedb.reggie Reggie …
9:44 AM PluginDownload edited by nicklas
Released Reggie 2.16.2 (diff)
9:44 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16.2 (diff)
9:42 AM reggie-2.16.2.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16.2
9:41 AM Changeset [2817] by nicklas
Tagging Reggie 2.16.2
9:40 AM Changeset [2816] by nicklas
Preparing to release Reggie 2.16.2
9:38 AM Ticket #665 (Display pool name in warning messages) closed by nicklas
fixed: (In [2815]) Fixes #665: Display pool name in warning messages
9:38 AM Changeset [2815] by nicklas
Fixes #665: Display pool name in warning messages
9:35 AM Changeset [2814] by nicklas
References #666: Default number of slots for demux should be 4 Same …
9:34 AM Ticket #666 (Default number of slots for demux should be 4) closed by nicklas
fixed: (In [2813]) Fixes #666: Default number of slots for demux should be 4
9:34 AM Changeset [2813] by nicklas
Fixes #666: Default number of slots for demux should be 4
9:33 AM Ticket #666 (Default number of slots for demux should be 4) created by nicklas
Tests have shown that this is good enough and leaves a lot of other …
9:14 AM Ticket #664 (Display pool names in confirm demux wizard) closed by nicklas
fixed: (In [2812]) Fixes #664: Display pool names in confirm demux wizard …
9:14 AM Changeset [2812] by nicklas
Fixes #664: Display pool names in confirm demux wizard Additional …
8:07 AM Ticket #665 (Display pool name in warning messages) created by nicklas
[…]
8:05 AM Ticket #664 (Display pool names in confirm demux wizard) created by nicklas
8:04 AM Ticket #663 (Demux script should not gzip FASTQ files until the last step) closed by nicklas
fixed: (In [2811]) Fixes #663: Demux script should not gzip FASTQ files until …
8:04 AM Changeset [2811] by nicklas
Fixes #663: Demux script should not gzip FASTQ files until the last step

Oct 15, 2014:

3:27 PM Ticket #662 (Race conditions in demux script) closed by nicklas
fixed: (In [2810]) Fixes #662: Race conditions in demux script This was …
3:27 PM Changeset [2810] by nicklas
Fixes #662: Race conditions in demux script This was caused by …
2:59 PM Ticket #663 (Demux script should not gzip FASTQ files until the last step) created by nicklas
This currently happens when merging the FASTQ files from the demux. …
2:56 PM Ticket #662 (Race conditions in demux script) created by nicklas
The demux script starts some of the steps in the background, but there …
2:07 PM Changeset [2809] by nicklas
References #630: Start cufflinks Must wait for the fix commands to …
1:18 PM Changeset [2808] by nicklas
References #640: Finalize update to new scripting pattern Changes …
1:11 PM Changeset [2807] by nicklas
References #630: Start cufflinks Added option to select an import …
10:29 AM Changeset [2806] by nicklas
References #630: Start cufflinks New tracking-id mapping file that is …
9:39 AM Changeset [2805] by nicklas
References #640: Finalize update to new scripting pattern Updated the …

Oct 14, 2014:

3:44 PM Ticket #661 (Calculate average fragment size and standard deviation after tophat) closed by nicklas
fixed: (In [2804]) Fixes #661: Calculate average fragment size and standard …
3:44 PM Changeset [2804] by nicklas
Fixes #661: Calculate average fragment size and standard deviation …
2:12 PM Changeset [2803] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:32 AM Ticket #661 (Calculate average fragment size and standard deviation after tophat) created by nicklas
This is the same as we already do in the demux step. But in this case …

Oct 13, 2014:

2:52 PM Changeset [2802] by nicklas
References #656: FASTQ files are not always stored in the expected …
2:49 PM Changeset [2801] by nicklas
Merge Reggie 2.16.1 to the trunk.
2:39 PM Changeset [2800] by nicklas
Preparing for future release Reggie 2.16.2
2:39 PM PluginDownload edited by nicklas
Released Reggie 2.16.1 (diff)
2:37 PM Milestone Reggie v2.16.1 completed
Bug fixes for Reggie 2.16. See [wiki:net.sf.basedb.reggie Reggie …
2:36 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16.1 (diff)
2:34 PM reggie-2.16.1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16.1
2:33 PM Changeset [2799] by nicklas
Tagging Reggie 2.16.1
2:32 PM Changeset [2798] by nicklas
Preparing to release Reggie 2.16.1
2:30 PM Ticket #660 (Error in sample source report wizard) closed by nicklas
fixed: (In [2797]) Fixes #660: Error in sample source report wizard
2:30 PM Changeset [2797] by nicklas
Fixes #660: Error in sample source report wizard
2:26 PM Ticket #660 (Error in sample source report wizard) created by nicklas
Go to the sample source report wizard. Select the 'Overview report' …
1:32 PM Changeset [2796] by nicklas
References #640: Finalize update to new scripting pattern Found some …
1:31 PM Changeset [2795] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:32 AM Changeset [2794] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
9:38 AM Changeset [2793] by nicklas
Synchronize changes from #653, #654, #658 and #659 to the trunk.
9:27 AM Changeset [2792] by nicklas
References #657: Include Reggie version number in wizards Added …
9:18 AM Ticket #659 (Do not trust fragement size calculated by bowtie if number of used ...) closed by nicklas
fixed: (In [2791]) Fixes #659: Do not trust fragement size calculated by …
9:18 AM Changeset [2791] by nicklas
Fixes #659: Do not trust fragement size calculated by bowtie if number …
9:14 AM Changeset [2790] by nicklas
References #657: Include Reggie version number in wizards Change …
9:12 AM Changeset [2789] by nicklas
Oh, that's just my pet snake, Reggie!
8:54 AM Ticket #659 (Do not trust fragement size calculated by bowtie if number of used ...) created by nicklas
The FragmentSizeAvg and FragmentSizeStd should be set to -1 if the …
8:51 AM Ticket #658 (Adjust fragment size mean and standard deviation) closed by nicklas
fixed: (In [2788]) Fixes #658: Adjust fragment size mean and standard …
8:51 AM Changeset [2788] by nicklas
Fixes #658: Adjust fragment size mean and standard deviation Added …
8:41 AM Changeset [2787] by nicklas
References #653: Use explicit paths to all important program used in …
7:42 AM Changeset [2786] by nicklas
References #653: Use explicit paths to all important program used in …

Oct 10, 2014:

2:23 PM Ticket #658 (Adjust fragment size mean and standard deviation) created by nicklas
In the demux step we introduced a call to bowtie that is used to …
12:59 PM Changeset [2785] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:55 AM Changeset [2784] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
11:14 AM Changeset [2783] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
10:59 AM Changeset [2782] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
9:17 AM Changeset [2781] by nicklas
Tag mismatch.
9:14 AM Ticket #657 (Include Reggie version number in wizards) closed by nicklas
fixed: (In [2780]) Fixes #657: Include Reggie version number in wizards …
9:14 AM Changeset [2780] by nicklas
Fixes #657: Include Reggie version number in wizards build.xml …
9:11 AM Ticket #657 (Include Reggie version number in wizards) created by nicklas
8:27 AM Ticket #656 (FASTQ files are not always stored in the expected folder) closed by nicklas
fixed: (In [2779]) Fixes #656: FASTQ files are not always stored in the …
8:27 AM Changeset [2779] by nicklas
Fixes #656: FASTQ files are not always stored in the expected folder …

Oct 9, 2014:

12:42 PM Changeset [2778] by olle
12:41 PM Changeset [2777] by olle
12:41 PM Changeset [2776] by olle
12:32 PM Changeset [2775] by olle
Registration extension for Melanoma/Lung? cancer project.
11:39 AM Changeset [2774] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
8:40 AM Changeset [2773] by nicklas
References #656: FASTQ files are not always stored in the expected …
8:13 AM Ticket #654 (Synchronize default options for pipeline analysis) closed by nicklas
fixed
8:13 AM Changeset [2772] by nicklas
References #654: Synchronize default options for pipeline analysis …
8:10 AM Changeset [2771] by nicklas
References #654: Synchronize default options for pipeline analysis …
8:09 AM Ticket #655 (PT_READS is not reported correctly in description for FASTQ files) closed by nicklas
fixed: (In [2770]) Fixes #655: PT_READS is not reported correctly in …
8:09 AM Changeset [2770] by nicklas
Fixes #655: PT_READS is not reported correctly in description for …

Oct 8, 2014:

9:46 PM Ticket #656 (FASTQ files are not always stored in the expected folder) created by nicklas
Expected: […] Actual: […] This difference is also mapped to …
9:41 PM Ticket #655 (PT_READS is not reported correctly in description for FASTQ files) created by nicklas
For example: 30803478 READS; 30803478 PF_READS; [J@11c2cada PT_READS
12:51 PM Ticket #653 (Use explicit paths to all important program used in pipeline) closed by nicklas
fixed: (In [2769]) Fixes #653: Use explicit paths to all important program …
12:51 PM Changeset [2769] by nicklas
Fixes #653: Use explicit paths to all important program used in …
11:59 AM Changeset [2768] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:52 AM Changeset [2767] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:49 AM Changeset [2766] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:48 AM Changeset [2765] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:45 AM Changeset [2764] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:43 AM Changeset [2763] by nicklas
References #654: Synchronize default options for pipeline analysis …
11:42 AM Ticket #654 (Synchronize default options for pipeline analysis) created by nicklas
The reggie-ogs-hosts.xml file contain a lot of options for the …
11:40 AM Changeset [2762] by nicklas
References #653: Use explicit paths to all important program used in …
11:37 AM Ticket #653 (Use explicit paths to all important program used in pipeline) created by nicklas
Eg. Tophat and bowtie. It is already possible to set a path in the …
9:40 AM Ticket #652 (New location of BASE JAR files) closed by nicklas
fixed: I guess that should be most of the BASE3-compatible plug-ins/extensions.
9:37 AM Changeset [2761] by nicklas
References #652: New location of BASE JAR files YubiKey? trunk.
9:35 AM Changeset [2760] by nicklas
References #652: New location of BASE JAR files X-files trunk.
9:34 AM Changeset [2759] by nicklas
References #652: New location of BASE JAR files Normalizers trunk.
9:33 AM Changeset [2758] by nicklas
References #652: New location of BASE JAR files MeV trunk.
9:32 AM Changeset [2757] by nicklas
References #652: New location of BASE JAR files LabEnv? trunk.
9:31 AM Changeset [2756] by nicklas
References #652: New location of BASE JAR files Illumina plug-ins trunk.
9:29 AM Changeset [2755] by nicklas
References #652: New location of BASE JAR files HDFS trunk.
9:27 AM Changeset [2754] by nicklas
References #652: New location of BASE JAR files Code examples trunk.
9:26 AM Changeset [2753] by nicklas
References #652: New location of BASE JAR files FTP Server trunk.
9:24 AM Changeset [2752] by nicklas
References #652: New location of BASE JAR files Reggie trunk. But …
9:23 AM Changeset [2751] by nicklas
References #652: New location of BASE JAR files Reggie 2.16-stable.
9:20 AM Ticket #652 (New location of BASE JAR files) created by nicklas
This affects all plug-ins that has implemented automatic download of …
9:12 AM Changeset [2750] by nicklas
References #630: Start cufflinks Added support for re-mapping some …
9:06 AM Changeset [2749] by nicklas
Adding script for replacing tracking_id values in the fpkm_tracking …
8:43 AM Ticket #651 (Add 1x16 pool schema to create mRNA plate wizard) created by nicklas
This schema is likely going to be used in the future. It may not …
8:35 AM Ticket #650 (New type of specimen core biopsy) created by nicklas
Taken between the first core biopsy and the operator. Referral form …
8:17 AM Ticket #649 (Better balance in progress when demuxing) closed by nicklas
fixed: (In [2748]) Fixes #649: Better balance in progress when demuxing
8:17 AM Changeset [2748] by nicklas
Fixes #649: Better balance in progress when demuxing
8:14 AM Ticket #649 (Better balance in progress when demuxing) created by nicklas
The current implementation assigns 50% of the progress to the demux …

Oct 7, 2014:

2:45 PM Changeset [2747] by nicklas
References #641: Import data from cufflinks result files Adding …
12:36 PM Ticket #646 (New options for specimen type in specimen tube registration) closed by nicklas
fixed: (In [2746]) Fixes #646: New options for specimen type in specimen tube …
12:36 PM Changeset [2746] by nicklas
Fixes #646: New options for specimen type in specimen tube registration
12:32 PM Ticket #646 (New options for specimen type in specimen tube registration) reopened by nicklas
12:32 PM Changeset [2745] by nicklas
References #640: Finalize update to new scripting pattern More …

Oct 6, 2014:

3:56 PM Ticket #647 (Select specimen type per tube in specimen tube registration) closed by nicklas
fixed: (In [2744]) Fixes #647: Select specimen type per tube in specimen tube …
3:56 PM Changeset [2744] by nicklas
Fixes #647: Select specimen type per tube in specimen tube registration
3:46 PM Ticket #648 (More help texts in the specimen tube registration wizard) closed by nicklas
fixed: (In [2743]) Fixes #648: More help texts in the specimen tube …
3:46 PM Changeset [2743] by nicklas
Fixes #648: More help texts in the specimen tube registration wizard
3:41 PM Ticket #646 (New options for specimen type in specimen tube registration) closed by nicklas
fixed: (In [2742]) Fixes #646: New option for specimen type in specimen tube …
3:41 PM Changeset [2742] by nicklas
Fixes #646: New option for specimen type in specimen tube registration
3:34 PM Ticket #648 (More help texts in the specimen tube registration wizard) created by nicklas
Add some help text for 'Other path note' and 'Operator delivery …
3:32 PM Ticket #647 (Select specimen type per tube in specimen tube registration) created by nicklas
In the current implementation, the specimen type is selected in the …
3:29 PM Ticket #646 (New options for specimen type in specimen tube registration) created by nicklas
Uncertain and Normal Installation wizard needs to be updated and the …
3:03 PM Ticket #645 (More than one parent item was found when starting align job) closed by nicklas
fixed: (In [2741]) Fixes #645: More than one parent item was found when …
3:03 PM Changeset [2741] by nicklas
Fixes #645: More than one parent item was found when starting align job
2:47 PM Ticket #645 (More than one parent item was found when starting align job) created by nicklas
When starting an align job for a library that has been merged from 2 …
2:31 PM Changeset [2740] by nicklas
References #640: Finalize update to new scripting pattern Updated the …
12:01 PM Changeset [2739] by nicklas
References #630. Check that values from the database such as paths and …
11:46 AM Ticket #644 (Can't start align job) closed by nicklas
fixed: (In [2738]) Fixes #644: Can't start align job
11:46 AM Changeset [2738] by nicklas
Fixes #644: Can't start align job
11:28 AM Ticket #644 (Can't start align job) created by nicklas
When submitting the job an error message is returned: […] I guess …
11:13 AM Ticket #643 (Pathology referral form registration doesn't validate RNA later time) closed by nicklas
fixed: (In [2737]) Fixes #643: Pathology referral form registration doesn't …
11:13 AM Changeset [2737] by nicklas
Fixes #643: Pathology referral form registration doesn't validate RNA …
11:10 AM Ticket #643 (Pathology referral form registration doesn't validate RNA later time) created by nicklas
Entering a date but no time for RNA later doesn't perform correct …
10:48 AM Changeset [2736] by nicklas
Merge Reggie 2.16 (final) to trunk.
10:02 AM Changeset [2735] by nicklas
Preparing for future release Reggie 2.16.1
9:58 AM Milestone Reggie v2.16 completed
Focus on adding support for "Secondary analysis" to Reggie. This means …
9:58 AM Ticket #530 (Display logs from temperature and humidity measurements) closed by nicklas
fixed
9:57 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16 (final) (diff)
9:56 AM reggie-2.16.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16
9:53 AM Changeset [2734] by nicklas
Tagging Reggie 2.16
9:52 AM Changeset [2733] by nicklas
Preparing to release Reggie 2.16 final.
9:49 AM Changeset [2732] by nicklas
Remove unused import.
9:48 AM Changeset [2731] by nicklas
Remove unused import.
9:48 AM Changeset [2730] by nicklas
References #547: Start Demux and Merge Add 'rm' commands in the …
8:26 AM Changeset [2729] by nicklas
References #547, #593 and #631. Check that values from the database …
7:52 AM Changeset [2728] by nicklas
References #548: Register Demux and Merge as ended Display '-' …

Oct 3, 2014:

1:53 PM Changeset [2727] by nicklas
References #593: Start masking and alignment Switches to hg38 in the …
1:52 PM Changeset [2726] by nicklas
References #630: Start Cufflinks Switches to hg38 in the default …
7:48 AM Changeset [2725] by nicklas
References #641: Import data from cufflinks result files Schedules a …

Oct 2, 2014:

2:22 PM Changeset [2724] by nicklas
References #641: Import data from cufflinks result files Install …
2:18 PM Changeset [2723] by nicklas
References #641: Import data from cufflinks result files Change BASE …
9:09 AM Changeset [2722] by nicklas
References #630: Start cufflinks Added possibility to select an array …

Oct 1, 2014:

4:11 PM Changeset [2721] by nicklas
References #630: Start cufflinks It is possible to start and run …
4:08 PM Ticket #642 (Confirm feature extraction as completed) created by nicklas
This wizard should be done after running cufflinks (#630) and …
4:03 PM Ticket #641 (Import data from cufflinks result files) created by nicklas
When Cufflinks has completed it has created isoforms.fpkm_tracking
3:56 PM Ticket #640 (Finalize update to new scripting pattern) created by nicklas
Finish what was started in #571.
3:53 PM Milestone Reggie v2.15.4 completed
Bug fixes for Reggie 2.15. See [wiki:net.sf.basedb.reggie Reggie …
2:08 PM Changeset [2720] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
2:06 PM Changeset [2719] by nicklas
References #637: Add annotations for lot numbers in the …
2:03 PM Changeset [2718] by nicklas
References #637: Add annotations for lot numbers in the …
1:17 PM Changeset [2717] by nicklas
References #637: Add annotations for lot numbers in the …
8:53 AM Changeset [2716] by nicklas
References #632: Increase max volume limit in pooling wizard to 20µl …

Sep 30, 2014:

2:53 PM Changeset [2715] by nicklas
References #533: Add secondary analysis section to Reggie …
1:07 PM Changeset [2714] by nicklas
Update classpath in Eclipse.
1:04 PM Changeset [2713] by nicklas
Deleting obsolete branch.
1:04 PM Changeset [2712] by nicklas
Deleting obsolete branch.
1:03 PM Changeset [2711] by nicklas
Switching trunk to Reggie 2.17-dev
1:01 PM Changeset [2710] by nicklas
Creating 2.16-stable branch since it should be close to final release …
12:37 PM Changeset [2709] by nicklas
References #533: Add secondary analysis section to Reggie Making …

Sep 29, 2014:

2:35 PM Changeset [2708] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
1:51 PM Ticket #639 (Case summary may throw ItemNotFoundException) closed by nicklas
fixed: (In [2707]) Fixes #639: Case summary may throw ItemNotFoundException?
1:51 PM Changeset [2707] by nicklas
Fixes #639: Case summary may throw ItemNotFoundException?
1:47 PM Ticket #639 (Case summary may throw ItemNotFoundException) created by nicklas
This is an intermittent error that can only happen soon after after …
1:29 PM Changeset [2706] by nicklas
References #593 and #595. Parse 'accepted_hits_picardmetrics.csv' and …
1:24 PM Changeset [2705] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
8:22 AM Changeset [2704] by nicklas
References #533: Add secondary analysis section to Reggie Failure to …

Sep 26, 2014:

2:06 PM net.sf.basedb.reggie edited by nicklas
(diff)
2:03 PM reggie-2.16-beta-4.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.16-beta-4
2:03 PM Changeset [2703] by nicklas
Tagging Reggie 2.16-beta-4 (second try)
2:02 PM Changeset [2702] by nicklas
Resetting debug flags.
1:59 PM Changeset [2701] by nicklas
Removed since I forgot to reset debug flags.
1:43 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.16-beta-4 (diff)
1:41 PM Changeset [2700] by nicklas
Tagging Reggie 2.16-beta-4
1:38 PM Changeset [2699] by nicklas
Preparing to release Reggie 2.16-beta-4

Sep 25, 2014:

12:48 PM Changeset [2698] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:47 AM Changeset [2697] by nicklas
References #593: Start masking and alignment Adding …
9:24 AM Changeset [2696] by nicklas
Adding script for fixing the unmapped.bam file generated by tophat so …

Sep 24, 2014:

4:34 PM Changeset [2695] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
4:21 PM Changeset [2694] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
4:13 PM Changeset [2693] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
1:22 PM Changeset [2692] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
12:30 PM Changeset [2691] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
9:53 AM Ticket #637 (Add annotations for lot numbers in the DNA/RNA/FlowThrough registration) closed by nicklas
fixed: (In [2690]) Fixes #637: Add annotations for lot numbers in the …
9:53 AM Changeset [2690] by nicklas
Fixes #637: Add annotations for lot numbers in the DNA/RNA/FlowThrough …

Sep 23, 2014:

3:40 PM Changeset [2689] by nicklas
References #547: Start Demux and Merge Splitting Trimmomatic into two …
12:56 PM Changeset [2688] by nicklas
References #571: Update Reggie to new scripting pattern (first step) …
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