Timeline
Oct 15, 2014:
- 3:27 PM Ticket #662 (Race conditions in demux script) closed by
- fixed: (In [2810]) Fixes #662: Race conditions in demux script This was …
- 3:27 PM Changeset [2810] by
- 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
- This currently happens when merging the FASTQ files from the demux. …
- 2:56 PM Ticket #662 (Race conditions in demux script) created by
- The demux script starts some of the steps in the background, but there …
- 2:07 PM Changeset [2809] by
- References #630: Start cufflinks Must wait for the fix commands to …
- 1:18 PM Changeset [2808] by
- References #640: Finalize update to new scripting pattern Changes …
- 1:11 PM Changeset [2807] by
- References #630: Start cufflinks Added option to select an import …
- 10:29 AM Changeset [2806] by
- References #630: Start cufflinks New tracking-id mapping file that is …
- 9:39 AM Changeset [2805] by
- 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
- fixed: (In [2804]) Fixes #661: Calculate average fragment size and standard …
- 3:44 PM Changeset [2804] by
- Fixes #661: Calculate average fragment size and standard deviation …
- 2:12 PM Changeset [2803] by
- 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
- 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
- References #656: FASTQ files are not always stored in the expected …
- 2:49 PM Changeset [2801] by
- Merge Reggie 2.16.1 to the trunk.
- 2:39 PM Changeset [2800] by
- Preparing for future release Reggie 2.16.2
- 2:39 PM PluginDownload edited by
- 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
- Released Reggie 2.16.1 (diff)
- 2:33 PM Changeset [2799] by
- Tagging Reggie 2.16.1
- 2:32 PM Changeset [2798] by
- Preparing to release Reggie 2.16.1
- 2:30 PM Ticket #660 (Error in sample source report wizard) closed by
- fixed: (In [2797]) Fixes #660: Error in sample source report wizard
- 2:30 PM Changeset [2797] by
- Fixes #660: Error in sample source report wizard
- 2:26 PM Ticket #660 (Error in sample source report wizard) created by
- Go to the sample source report wizard. Select the 'Overview report' …
- 1:32 PM Changeset [2796] by
- References #640: Finalize update to new scripting pattern Found some …
- 1:31 PM Changeset [2795] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:32 AM Changeset [2794] by
- References #640: Finalize update to new scripting pattern Updated the …
- 9:38 AM Changeset [2793] by
- Synchronize changes from #653, #654, #658 and #659 to the trunk.
- 9:27 AM Changeset [2792] by
- 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
- fixed: (In [2791]) Fixes #659: Do not trust fragement size calculated by …
- 9:18 AM Changeset [2791] by
- Fixes #659: Do not trust fragement size calculated by bowtie if number …
- 9:14 AM Changeset [2790] by
- References #657: Include Reggie version number in wizards Change …
- 9:12 AM Changeset [2789] by
- 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
-
The
FragmentSizeAvgandFragmentSizeStdshould be set to -1 if the … - 8:51 AM Ticket #658 (Adjust fragment size mean and standard deviation) closed by
- fixed: (In [2788]) Fixes #658: Adjust fragment size mean and standard …
- 8:51 AM Changeset [2788] by
- Fixes #658: Adjust fragment size mean and standard deviation Added …
- 8:41 AM Changeset [2787] by
- References #653: Use explicit paths to all important program used in …
- 7:42 AM Changeset [2786] by
- 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
- In the demux step we introduced a call to bowtie that is used to …
- 12:59 PM Changeset [2785] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:55 AM Changeset [2784] by
- References #640: Finalize update to new scripting pattern Updated the …
- 11:14 AM Changeset [2783] by
- References #640: Finalize update to new scripting pattern Updated the …
- 10:59 AM Changeset [2782] by
- References #640: Finalize update to new scripting pattern Updated the …
- 9:17 AM Changeset [2781] by
- Tag mismatch.
- 9:14 AM Ticket #657 (Include Reggie version number in wizards) closed by
- fixed: (In [2780]) Fixes #657: Include Reggie version number in wizards …
- 9:14 AM Changeset [2780] by
- Fixes #657: Include Reggie version number in wizards build.xml …
- 9:11 AM Ticket #657 (Include Reggie version number in wizards) created by
- 8:27 AM Ticket #656 (FASTQ files are not always stored in the expected folder) closed by
- fixed: (In [2779]) Fixes #656: FASTQ files are not always stored in the …
- 8:27 AM Changeset [2779] by
- Fixes #656: FASTQ files are not always stored in the expected folder …
Oct 9, 2014:
- 12:42 PM Changeset [2778] by
- 12:41 PM Changeset [2777] by
- 12:41 PM Changeset [2776] by
- 12:32 PM Changeset [2775] by
- Registration extension for Melanoma/Lung? cancer project.
- 11:39 AM Changeset [2774] by
- References #640: Finalize update to new scripting pattern Updated the …
- 8:40 AM Changeset [2773] by
- References #656: FASTQ files are not always stored in the expected …
- 8:13 AM Ticket #654 (Synchronize default options for pipeline analysis) closed by
- fixed
- 8:13 AM Changeset [2772] by
- References #654: Synchronize default options for pipeline analysis …
- 8:10 AM Changeset [2771] by
- 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
- fixed: (In [2770]) Fixes #655: PT_READS is not reported correctly in …
- 8:09 AM Changeset [2770] by
- 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
- 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
- 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
- fixed: (In [2769]) Fixes #653: Use explicit paths to all important program …
- 12:51 PM Changeset [2769] by
- Fixes #653: Use explicit paths to all important program used in …
- 11:59 AM Changeset [2768] by
- References #654: Synchronize default options for pipeline analysis …
- 11:52 AM Changeset [2767] by
- References #654: Synchronize default options for pipeline analysis …
- 11:49 AM Changeset [2766] by
- References #654: Synchronize default options for pipeline analysis …
- 11:48 AM Changeset [2765] by
- References #654: Synchronize default options for pipeline analysis …
- 11:45 AM Changeset [2764] by
- References #654: Synchronize default options for pipeline analysis …
- 11:43 AM Changeset [2763] by
- References #654: Synchronize default options for pipeline analysis …
- 11:42 AM Ticket #654 (Synchronize default options for pipeline analysis) created by
- The reggie-ogs-hosts.xml file contain a lot of options for the …
- 11:40 AM Changeset [2762] by
- 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
- 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
- fixed: I guess that should be most of the BASE3-compatible plug-ins/extensions.
- 9:37 AM Changeset [2761] by
- References #652: New location of BASE JAR files YubiKey? trunk.
- 9:35 AM Changeset [2760] by
- References #652: New location of BASE JAR files X-files trunk.
- 9:34 AM Changeset [2759] by
- References #652: New location of BASE JAR files Normalizers trunk.
- 9:33 AM Changeset [2758] by
- References #652: New location of BASE JAR files MeV trunk.
- 9:32 AM Changeset [2757] by
- References #652: New location of BASE JAR files LabEnv? trunk.
- 9:31 AM Changeset [2756] by
- References #652: New location of BASE JAR files Illumina plug-ins trunk.
- 9:29 AM Changeset [2755] by
- References #652: New location of BASE JAR files HDFS trunk.
- 9:27 AM Changeset [2754] by
- References #652: New location of BASE JAR files Code examples trunk.
- 9:26 AM Changeset [2753] by
- References #652: New location of BASE JAR files FTP Server trunk.
- 9:24 AM Changeset [2752] by
- References #652: New location of BASE JAR files Reggie trunk. But …
- 9:23 AM Changeset [2751] by
- 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
- This affects all plug-ins that has implemented automatic download of …
- 9:12 AM Changeset [2750] by
- References #630: Start cufflinks Added support for re-mapping some …
- 9:06 AM Changeset [2749] by
- 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
- 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
- Taken between the first core biopsy and the operator. Referral form …
- 8:17 AM Ticket #649 (Better balance in progress when demuxing) closed by
- fixed: (In [2748]) Fixes #649: Better balance in progress when demuxing
- 8:17 AM Changeset [2748] by
- Fixes #649: Better balance in progress when demuxing
- 8:14 AM Ticket #649 (Better balance in progress when demuxing) created by
- The current implementation assigns 50% of the progress to the demux …
Oct 7, 2014:
- 2:45 PM Changeset [2747] by
- 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
- fixed: (In [2746]) Fixes #646: New options for specimen type in specimen tube …
- 12:36 PM Changeset [2746] by
- 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
- 12:32 PM Changeset [2745] by
- 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
- fixed: (In [2744]) Fixes #647: Select specimen type per tube in specimen tube …
- 3:56 PM Changeset [2744] by
- 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
- fixed: (In [2743]) Fixes #648: More help texts in the specimen tube …
- 3:46 PM Changeset [2743] by
- 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
- fixed: (In [2742]) Fixes #646: New option for specimen type in specimen tube …
- 3:41 PM Changeset [2742] by
- 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
- 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
- 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
- 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
- fixed: (In [2741]) Fixes #645: More than one parent item was found when …
- 3:03 PM Changeset [2741] by
- 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
- When starting an align job for a library that has been merged from 2 …
- 2:31 PM Changeset [2740] by
- References #640: Finalize update to new scripting pattern Updated the …
- 12:01 PM Changeset [2739] by
- References #630. Check that values from the database such as paths and …
- 11:46 AM Ticket #644 (Can't start align job) closed by
- fixed: (In [2738]) Fixes #644: Can't start align job
- 11:46 AM Changeset [2738] by
- Fixes #644: Can't start align job
- 11:28 AM Ticket #644 (Can't start align job) created by
- 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
- fixed: (In [2737]) Fixes #643: Pathology referral form registration doesn't …
- 11:13 AM Changeset [2737] by
- 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
- Entering a date but no time for RNA later doesn't perform correct …
- 10:48 AM Changeset [2736] by
- Merge Reggie 2.16 (final) to trunk.
- 10:02 AM Changeset [2735] by
- 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
- fixed
- 9:57 AM net.sf.basedb.reggie edited by
- Released Reggie 2.16 (final) (diff)
- 9:53 AM Changeset [2734] by
- Tagging Reggie 2.16
- 9:52 AM Changeset [2733] by
- Preparing to release Reggie 2.16 final.
- 9:49 AM Changeset [2732] by
- Remove unused import.
- 9:48 AM Changeset [2731] by
- Remove unused import.
- 9:48 AM Changeset [2730] by
- References #547: Start Demux and Merge Add 'rm' commands in the …
- 8:26 AM Changeset [2729] by
- References #547, #593 and #631. Check that values from the database …
- 7:52 AM Changeset [2728] by
- References #548: Register Demux and Merge as ended Display '-' …
Oct 3, 2014:
- 1:53 PM Changeset [2727] by
- References #593: Start masking and alignment Switches to hg38 in the …
- 1:52 PM Changeset [2726] by
- References #630: Start Cufflinks Switches to hg38 in the default …
- 7:48 AM Changeset [2725] by
- References #641: Import data from cufflinks result files Schedules a …
Oct 2, 2014:
- 2:22 PM Changeset [2724] by
- References #641: Import data from cufflinks result files Install …
- 2:18 PM Changeset [2723] by
- References #641: Import data from cufflinks result files Change BASE …
- 9:09 AM Changeset [2722] by
- References #630: Start cufflinks Added possibility to select an array …
Oct 1, 2014:
- 4:11 PM Changeset [2721] by
- References #630: Start cufflinks It is possible to start and run …
- 4:08 PM Ticket #642 (Confirm feature extraction as completed) created by
- This wizard should be done after running cufflinks (#630) and …
- 4:03 PM Ticket #641 (Import data from cufflinks result files) created by
-
When Cufflinks has completed it has created
isoforms.fpkm_tracking… - 3:56 PM Ticket #640 (Finalize update to new scripting pattern) created by
- 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
- References #571: Update Reggie to new scripting pattern (first step) …
- 2:06 PM Changeset [2719] by
- References #637: Add annotations for lot numbers in the …
- 2:03 PM Changeset [2718] by
- References #637: Add annotations for lot numbers in the …
- 1:17 PM Changeset [2717] by
- References #637: Add annotations for lot numbers in the …
- 8:53 AM Changeset [2716] by
- References #632: Increase max volume limit in pooling wizard to 20µl …
Sep 30, 2014:
- 2:53 PM Changeset [2715] by
- References #533: Add secondary analysis section to Reggie …
- 1:07 PM Changeset [2714] by
- Update classpath in Eclipse.
- 1:04 PM Changeset [2713] by
- Deleting obsolete branch.
- 1:04 PM Changeset [2712] by
- Deleting obsolete branch.
- 1:03 PM Changeset [2711] by
- Switching trunk to Reggie 2.17-dev
- 1:01 PM Changeset [2710] by
- Creating 2.16-stable branch since it should be close to final release …
- 12:37 PM Changeset [2709] by
- References #533: Add secondary analysis section to Reggie Making …
Sep 29, 2014:
- 2:35 PM Changeset [2708] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 1:51 PM Ticket #639 (Case summary may throw ItemNotFoundException) closed by
- fixed: (In [2707]) Fixes #639: Case summary may throw ItemNotFoundException?
- 1:51 PM Changeset [2707] by
- Fixes #639: Case summary may throw ItemNotFoundException?
- 1:47 PM Ticket #639 (Case summary may throw ItemNotFoundException) created by
- This is an intermittent error that can only happen soon after after …
- 1:29 PM Changeset [2706] by
- References #593 and #595. Parse 'accepted_hits_picardmetrics.csv' and …
- 1:24 PM Changeset [2705] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 8:22 AM Changeset [2704] by
- References #533: Add secondary analysis section to Reggie Failure to …
Sep 26, 2014:
- 2:06 PM net.sf.basedb.reggie edited by
- (diff)
- 2:03 PM Changeset [2703] by
- Tagging Reggie 2.16-beta-4 (second try)
- 2:02 PM Changeset [2702] by
- Resetting debug flags.
- 1:59 PM Changeset [2701] by
- Removed since I forgot to reset debug flags.
- 1:43 PM net.sf.basedb.reggie edited by
- Released Reggie 2.16-beta-4 (diff)
- 1:41 PM Changeset [2700] by
- Tagging Reggie 2.16-beta-4
- 1:38 PM Changeset [2699] by
- Preparing to release Reggie 2.16-beta-4
Sep 25, 2014:
- 12:48 PM Changeset [2698] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 9:47 AM Changeset [2697] by
- References #593: Start masking and alignment Adding …
- 9:24 AM Changeset [2696] by
- Adding script for fixing the unmapped.bam file generated by tophat so …
Sep 24, 2014:
- 4:34 PM Changeset [2695] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 4:21 PM Changeset [2694] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 4:13 PM Changeset [2693] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 1:22 PM Changeset [2692] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 12:30 PM Changeset [2691] by
- 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
- fixed: (In [2690]) Fixes #637: Add annotations for lot numbers in the …
- 9:53 AM Changeset [2690] by
- Fixes #637: Add annotations for lot numbers in the DNA/RNA/FlowThrough …
Sep 23, 2014:
- 3:40 PM Changeset [2689] by
- References #547: Start Demux and Merge Splitting Trimmomatic into two …
- 12:56 PM Changeset [2688] by
- References #571: Update Reggie to new scripting pattern (first step) …
Sep 22, 2014:
- 9:02 AM Changeset [2687] by
- References #637: Add annotations for lot numbers in the …
- 8:30 AM Changeset [2686] by
- References #571: Update Reggie to new scripting pattern (first step) …
Sep 19, 2014:
- 2:44 PM Ticket #638 (Fix issues with not filling all pools on a a plate) created by
- For testing and evaluation purposes it is sometimes desirable to …
- 7:58 AM Changeset [2685] by
- References #595: Confirm alignment Same change as [2683] for the …
Sep 18, 2014:
- 4:03 PM Changeset [2684] by
- References #593: Start masking and alignment Use the average fragment …
- 2:37 PM Changeset [2683] by
- References #548: Register Demux and Merge as ended Also delete file …
- 1:36 PM Changeset [2682] by
- References #548: Register Demux and Merge as ended Display calculated …
- 11:22 AM Changeset [2681] by
- References #548: Register Demux and Merge as ended Selecting …
- 11:19 AM Changeset [2680] by
- References #547: Start Demux and Merge Calling bowtie to align a …
- 11:13 AM Changeset [2679] by
- Adding script for calculating average of fragment lengths.
- 8:04 AM Changeset [2678] by
- References #571: Update Reggie to new scripting pattern (first step) …
Sep 17, 2014:
- 4:09 PM Changeset [2677] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 10:49 AM Changeset [2676] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 10:04 AM Ticket #637 (Add annotations for lot numbers in the DNA/RNA/FlowThrough registration) created by
- We would like to keep track of the lot numbers for some reagents used …
- 9:47 AM Changeset [2675] by
- References #571: Update Reggie to new scripting pattern (first step) …
Sep 16, 2014:
- 2:28 PM Ticket #636 (INCA export may fail if there are blood samples with missing date) closed by
- fixed: (In [2674]) Fixes #636: INCA export may fail if there are blood …
- 2:28 PM Changeset [2674] by
- Fixes #636: INCA export may fail if there are blood samples with …
- 1:18 PM Ticket #636 (INCA export may fail if there are blood samples with missing date) created by
- The INCA export fail in this scenario: * "all" option is selected * …
- 8:48 AM Changeset [2673] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 7:52 AM Changeset [2672] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 7:49 AM Changeset [2671] by
- References #571: Update Reggie to new scripting pattern (first step) …
Sep 15, 2014:
- 4:05 PM Ticket #635 (Include analysis information in the case summary) created by
- The case summary currently goes down to 'Sequencing run' items. We …
- 4:00 PM Ticket #634 (Retraction wizard) closed by
- duplicate: This ticket turned out to be a duplicate of Ticket #526 "Retraction …
- 3:54 PM Changeset [2670] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 3:47 PM Changeset [2669] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 2:47 PM Changeset [2668] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 1:10 PM Changeset [2667] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 12:48 PM Changeset [2666] by
- References #571: Update Reggie to new scripting pattern (first step) …
- 12:21 PM Ticket #634 (Retraction wizard) created by
- A wizard should be created to support retraction of data for a …
- 9:00 AM Changeset [2665] by
- Fixed incorrect message.
- 8:23 AM Changeset [2664] by
- References #571: Update Reggie to new scripting pattern (first step) …
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