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Ticket Summary Owner Type Priority Milestone Component
#594 Changes for NextSeq support Nicklas Nordborg enhancement major Reggie v2.15.1 net.sf.basedb.reggie
#595 Confirm alignment Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#596 Import adapter peak information when registering libraries Nicklas Nordborg enhancement major Reggie v2.15.2 net.sf.basedb.reggie
#597 Display adapter peak fraction in the pooling wizard Nicklas Nordborg enhancement major Reggie v2.15.2 net.sf.basedb.reggie
#598 Pooling wizard can't show flag and warning at the same time Nicklas Nordborg defect major Reggie v2.15.3 net.sf.basedb.reggie
#599 YubiKey package is missing yubikey-extended-properties.xml Nicklas Nordborg defect major YubiKey v1.1 net.sf.basedb.yubikey
#600 Installation instructions for YubiKey extensions is not clear Nicklas Nordborg enhancement major YubiKey v1.1 net.sf.basedb.yubikey
#601 NullPointerException when trying to assign a YubiKey to a new user Nicklas Nordborg defect major YubiKey v1.1 net.sf.basedb.yubikey
#604 New wizard "RNA dilution registration" Nicklas Nordborg task major Reggie v2.15.3 net.sf.basedb.reggie
#605 Switch to JDOM 2 Nicklas Nordborg task major Reggie v3.0 net.sf.basedb.reggie
#608 Update Labenv to new scripting pattern olle enhancement major LabEnv v1.3 net.sf.basedb.labenv
#609 Add support for ignoring YubiKey login depending on client Nicklas Nordborg enhancement major YubiKey v1.1 net.sf.basedb.yubikey
#611 Create package for supporting external files via SFTP Nicklas Nordborg task major External files support 1.0 net.sf.basedb.xfiles
#612 LabEnv overview display shows wrong time offsets when the latest data points are filtered away olle defect major LabEnv v1.2 net.sf.basedb.labenv
#614 Improve error handling when executing jobs on the cluster Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#615 Lab environment extension stability improvement and bug fixes for v1.1 olle enhancement major LabEnv v1.2 net.sf.basedb.labenv
#616 External files with a file server can't be downloaded Nicklas Nordborg defect major FTP Server v1.4 net.sf.basedb.ftp
#617 Re-use server connections within a transaction Nicklas Nordborg enhancement major External files support 1.1 net.sf.basedb.xfiles
#618 Specimen tube item is registered with incorrect name Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#621 Second specimen tube is not linked if registered before pathology referral Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#629 Use annotations on protocols in the demux and mask/align step to set some program parameters Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#631 Add data check to the confirm sequencing ended wizard Nicklas Nordborg enhancement major Reggie v2.16 net.sf.basedb.reggie
#634 Retraction wizard olle enhancement major net.sf.basedb.reggie
#635 Include analysis information in the case summary Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#636 INCA export may fail if there are blood samples with missing date Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#637 Add annotations for lot numbers in the DNA/RNA/FlowThrough registration Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#638 Fix issues with not filling all pools on a a plate Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#640 Finalize update to new scripting pattern Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#642 Confirm feature extraction as completed Nicklas Nordborg task major Reggie v2.17 net.sf.basedb.reggie
#646 New options for specimen type in specimen tube registration Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#647 Select specimen type per tube in specimen tube registration Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#650 New type of specimen core biopsy Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#651 Add 1x16 pool schema to create mRNA plate wizard Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#653 Use explicit paths to all important program used in pipeline Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#655 PT_READS is not reported correctly in description for FASTQ files Nicklas Nordborg defect major Reggie v2.16.1 net.sf.basedb.reggie
#659 Do not trust fragement size calculated by bowtie if number of used fragments is too low Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#660 Error in sample source report wizard Nicklas Nordborg defect major Reggie v2.16.1 net.sf.basedb.reggie
#661 Calculate average fragment size and standard deviation after tophat Nicklas Nordborg enhancement major Reggie v2.16.2 net.sf.basedb.reggie
#663 Demux script should not gzip FASTQ files until the last step Nicklas Nordborg enhancement major Reggie v2.16.2 net.sf.basedb.reggie
#671 Save reggie version with jobs Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#678 Operator delivery comment in specimen tube registration wizard is not saved Nicklas Nordborg defect major Reggie v2.17 net.sf.basedb.reggie
#679 Configuration file improvments Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#681 Run CheckIlluminaDirectory from a cluster node instead of the cluster controller Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#682 Improve performance when submitting jobs to cluster Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#683 Do not start processes in the background Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#684 Run picard AddOrReplaceReadGroups after alignment Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#687 ApWeight field in partition wizard doesn't auto-tab on ENTER key Nicklas Nordborg defect major Reggie v2.17.1 net.sf.basedb.reggie
#688 Depend on BASE 3.3.3 Nicklas Nordborg task major Reggie v2.17.1 net.sf.basedb.reggie
#689 Use new script for checking Illumina data files Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#690 MeLuDi - Registration wizard for melanoma-lung cancer projects olle task major MeLuDi v1.0 net.sf.basedb.meludi
#699 Library registration doesn't warn about missing values in Caliper well table CSV Nicklas Nordborg defect major Reggie v2.17.2 net.sf.basedb.reggie
#700 Missing '-' between plate name and library name in start alignment and start cufflinks wizards Nicklas Nordborg defect major Reggie v2.17.3 net.sf.basedb.reggie
#701 Check compability with BASE 3.4 Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#702 Use skin features in BASE 3.4 Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#703 Make print package compatible with skins Nicklas Nordborg enhancement major Print package v1.2 net.sf.basedb.print
#704 NullPointerException in retraction servlet when entering a case name that doesn't exist Nicklas Nordborg defect major Reggie v2.18 net.sf.basedb.reggie
#706 Update LabEnv to use BASE database capabilties instead of SQLite Nicklas Nordborg task major LabEnv v1.3 net.sf.basedb.labenv
#707 Switch to Slf4j Nicklas Nordborg enhancement major Example code v1.7 net.sf.basedb.examplecode
#708 Add example skin Nicklas Nordborg task major Example code v1.7 net.sf.basedb.examplecode
#713 Comment for bioplate in RNA dilution registration is not updated Nicklas Nordborg defect major Reggie v2.18.1 net.sf.basedb.reggie
#716 Add support for Reggie to the gold skin enhancement major Skin-collection 1.1 net.sf.basedb.skincollection
#718 MeLuDi v.1.0 bug fixes and improvements olle task major MeLuDi v1.1 net.sf.basedb.meludi
#720 Change major Reggie version to 3 Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#723 Retraction wizard - Step 2: Follow up olle task major Reggie v3.0 net.sf.basedb.reggie
#725 MeLuDi v.1.1 bug fixes and improvements olle task major MeLuDi v1.2 net.sf.basedb.meludi
#726 Improve performance of counter on index page Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#728 Get rid of SQLite olle task major LabEnv v1.4 net.sf.basedb.labenv
#730 Set target molarity in "Create pooled libraries" wizard Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#732 Software item on aligned sequences is not set Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#733 The create pools wizard create pools with roman numerals as name Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#734 The create new mRNA plate wizard should reset RNA marked for re-processing Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#735 Can't modify number of slides created in the HE glass registration wizard Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#736 Some HE glass may be stained with something else than HE Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#742 Detect tiles with empty barcode files Nicklas Nordborg task major Reggie v3.2 net.sf.basedb.reggie
#746 IHC-quality annotation Nicklas Nordborg enhancement major Reggie v3.2 net.sf.basedb.reggie
#754 Make case summary display more tolerant aginst problems Nicklas Nordborg enhancement major Reggie v3.2.1 net.sf.basedb.reggie
#756 Display numbers with two decimals in the Flagged RNA wizard Nicklas Nordborg enhancement major Reggie v3.2.1 net.sf.basedb.reggie
#758 Open grid sceduler jobs with no job id in BASE Nicklas Nordborg defect major Reggie v3.2.1 net.sf.basedb.reggie
#759 MeLuDi v.1.2 bug fixes and improvements olle task major MeLuDI v1.2.1 net.sf.basedb.meludi
#762 Pre-normalization changes due to NeoPrep Nicklas Nordborg task major Reggie v3.4 net.sf.basedb.reggie
#763 Change limit for NotEnoughRemaininQuantity flag in the extraction wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#764 Support for neoprep in the library preparation Nicklas Nordborg task major Reggie v3.4 net.sf.basedb.reggie
#765 Add 3x16 pool schema to create mRNA plate wizard Nicklas Nordborg enhancement major Reggie v3.2.2 net.sf.basedb.reggie
#767 MeLuDI v.1.2.1 bug fixes and improvements olle task major MeLuDI v1.2.2 net.sf.basedb.meludi
#768 MeLuDI v.1.2.2 bug fixes and improvements olle task major MeLuDI v1.2.3 net.sf.basedb.meludi
#769 Retraction wizard - Additions to Step 2: Follow up olle task major Reggie v3.4 net.sf.basedb.reggie
#770 Retraction wizard - Step 3: Destruction olle task major Reggie v4.2 net.sf.basedb.reggie
#771 Yellow label highlighting a representative specimen Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#772 New sample annotation (LinkedSpecimen) to highlight prior specimen Nicklas Nordborg task major Reggie v3.5 net.sf.basedb.reggie
#774 Comment for bioplate in mRNA registration is not updated Nicklas Nordborg defect major Reggie v3.3.1 net.sf.basedb.reggie
#777 MeLuDI v.1.2.3 bug fixes and improvements olle task major MeLuDI v1.2.4 net.sf.basedb.meludi
#779 Librararies with very high molarity gives "Low molarity" warning in pooling wizard Nicklas Nordborg defect major Reggie v3.4 net.sf.basedb.reggie
#780 Redesign Reggie start page Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#781 Clean up code in retraction wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#783 Switch to Java 8 Nicklas Nordborg enhancement major Reggie v4.0 net.sf.basedb.reggie
#786 MeLuDI v.1.2.4 bug fixes and improvements olle task major MeLuDI v1.2.5 net.sf.basedb.meludi
#787 Add support for BloodDNA items olle task major Reggie v3.4 net.sf.basedb.reggie
#789 LabEnv links in Case Summary do not work with BASE 3.5 olle defect major LabEnv v1.4 net.sf.basedb.labenv
#790 Add new site: Jönköping Nicklas Nordborg task major Reggie v3.5 net.sf.basedb.reggie
#791 Upload microscope images in the histology scoring wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
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