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Ticket Summary Owner Type Priority Milestone Component
#814 New 1x16 pool layout that is offset to the left Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#817 Always display rna box position in normalization protocol Nicklas Nordborg enhancement trivial Reggie v3.7 net.sf.basedb.reggie
#818 Track volumes of RNAQC aliquots Nicklas Nordborg enhancement major Reggie v3.7 net.sf.basedb.reggie
#819 Printable lab protocol from Create aliquots on Bioanalyzer/Caliper plates wizard Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#820 Add "Inconclusive" as an option to the IHCQuality annotation Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#821 Remote registration of RunParameters.xml in Register sequencing started wizard Nicklas Nordborg enhancement major Reggie v3.7 net.sf.basedb.reggie
#822 Fix character encoding problems with R scripts Nicklas Nordborg enhancement critical Reggie v3.7.1 net.sf.basedb.reggie
#782 Fix compilation error when compiling against BASE 3.6 Nicklas Nordborg task critical Reggie v4.0 net.sf.basedb.reggie
#783 Switch to Java 8 Nicklas Nordborg enhancement major Reggie v4.0 net.sf.basedb.reggie
#785 Separate project archive folder for external samples Nicklas Nordborg enhancement critical Reggie v4.0 net.sf.basedb.reggie
#823 Do not include items with only Read permission in selection lists Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#824 fix_tophat_unmapped_reads.py has been renamed to tophat-recondition.py Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#825 Optimize library preparation and sequencing wizards for NextSeq Nicklas Nordborg enhancement blocker Reggie v4.0 net.sf.basedb.reggie
#826 Auto-create mRNA plate wizard Nicklas Nordborg task major Reggie v4.0 net.sf.basedb.reggie
#827 Implement support for YellowLabel in the specimen tube registration wizard Nicklas Nordborg enhancement critical Reggie v4.0 net.sf.basedb.reggie
#828 PoolSchema=1by16offset is not installed by the installation wizard Nicklas Nordborg defect major Reggie v4.0 net.sf.basedb.reggie
#829 Display RNA box position in the lab protocol from "Create aliquots on Bioanalyzer/Caliper plates" wizard Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#830 Link software items to gene and pilot report pdf files Nicklas Nordborg enhancement major Reggie v4.0 net.sf.basedb.reggie
#831 Losing connection to Open grid cluster Nicklas Nordborg defect minor Reggie v4.0 net.sf.basedb.reggie
#832 Specimen tube registration wizard should create new storage boxes Nicklas Nordborg task minor Reggie v4.0 net.sf.basedb.reggie
#833 The "Plasma/serum" checkbox in the Blood referral form registration wizard (step 3) should not be checked for site '99' Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#801 MeLuDI library preparation wizards first version olle task major MeLuDI v1.4.0 net.sf.basedb.meludi
#816 MeLuDI v.1.3.3 bug fixes and improvements olle task major MeLuDI v1.4.0 net.sf.basedb.meludi
#836 MeLuDI v.1.4.0 bug fixes and improvements olle task major MeLuDI v1.4.1 net.sf.basedb.meludi
#837 MeLuDI v.1.4.1 bug fixes and improvements olle task major MeLuDI v1.4.2 net.sf.basedb.meludi
#728 Get rid of SQLite olle task major LabEnv v1.4 net.sf.basedb.labenv
#789 LabEnv links in Case Summary do not work with BASE 3.5 olle defect major LabEnv v1.4 net.sf.basedb.labenv
#843 Set <max-base-version> to 3.8.0 olle task minor LabEnv v1.4 net.sf.basedb.labenv
#844 Switch to Java 8 olle enhancement major LabEnv v1.4 net.sf.basedb.labenv
#845 Remove LabEnv references to Reggie olle task major LabEnv v1.4 net.sf.basedb.labenv
#834 Auto-analyze when sequencing has ended Nicklas Nordborg task critical Reggie v4.1 net.sf.basedb.reggie
#835 Manual normalization with NeoPrep Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#838 Partial confirmation of demux job Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#839 Change YellowLabel status in "Pathology referral form registration" wizard Nicklas Nordborg enhancement minor Reggie v4.1 net.sf.basedb.reggie
#840 Change cutoff for Caliper HiSense to 50ng/µl Nicklas Nordborg enhancement trivial Reggie v4.1 net.sf.basedb.reggie
#841 Change required BASE version to BASE 3.7 Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#846 Highlight YellowLabel specimen in sample processing wizards Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#848 Enabled/disable experimental features in reggie-config.xml Nicklas Nordborg task major Reggie v4.1 net.sf.basedb.reggie
#850 Encoding problems with JSON data Nicklas Nordborg defect blocker Reggie v4.1.1 net.sf.basedb.reggie
#770 Retraction wizard - Step 3: Destruction olle task major Reggie v4.2 net.sf.basedb.reggie
#847 Highlight YellowLabel specimen in library preparation wizards Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#849 Demux wizard doesn't check that items have names that are accepted by downstream analysis steps Nicklas Nordborg defect major Reggie v4.2 net.sf.basedb.reggie
#851 Retraction wizard - Step 2: Follow up should allow dates to be set as N/A olle task major Reggie v4.2 net.sf.basedb.reggie
#852 Highlight YellowLabel specimen case summary Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#853 RNA marked for ReProcess should be auto-selected even if no RNAQC child item exists Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#854 Fix "Remaining quantity" filter in "Manual select" function Nicklas Nordborg defect minor Reggie v4.2 net.sf.basedb.reggie
#855 Retraction follow-up and destruction wizards should make it easier to select existing cases Nicklas Nordborg task major Reggie v4.2 net.sf.basedb.reggie
#856 Highlight YellowLabel specimen in secondary analysis wizards Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#857 Highlight YellowLabel specimen in Flagged RNA wizard Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#858 Target volume for NeoPrep should be changed from 45 to 12.5 Nicklas Nordborg task major Reggie v4.2 net.sf.basedb.reggie
#859 ProjectArchive should be shared with USE permission to the project Nicklas Nordborg enhancement minor Reggie v4.2 net.sf.basedb.reggie
#860 NeoPrep need other barcode variants Nicklas Nordborg defect major Reggie v4.2.1 net.sf.basedb.reggie
#862 Import frozen tissue date wizard should have PatientCurator role Nicklas Nordborg defect minor Reggie v4.2.1 net.sf.basedb.reggie
#871 NullPointerException when selecting a software item in the gene/pilot report wizard Nicklas Nordborg defect major Reggie v4.2.1 net.sf.basedb.reggie
#873 Target volume for NeoPrep should be changed from 12.5 to 15 Nicklas Nordborg enhancement major Reggie v4.2.1 net.sf.basedb.reggie
#868 Update SSH library Nicklas Nordborg enhancement major External files support 1.2 net.sf.basedb.xfiles
#869 Switch to Java 8 Nicklas Nordborg task major External files support 1.2 net.sf.basedb.xfiles
#870 Switch to BASE 3.7 Nicklas Nordborg task major External files support 1.2 net.sf.basedb.xfiles
#771 Yellow label highlighting a representative specimen Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#861 YellowLabel tracking wizard Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#863 Secondary analysis scripts should set permissions on created files in ProjectArchive Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#864 Implement a service that check and update file permission in ProjectArchive Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#865 Stray files wizard Nicklas Nordborg task major Reggie v4.3 net.sf.basedb.reggie
#867 Update SSH library Nicklas Nordborg enhancement major Reggie v4.3 net.sf.basedb.reggie
#874 <reference-gidx> is incorrect in the default reggie-config.xml file Nicklas Nordborg defect major Reggie v4.3 net.sf.basedb.reggie
#875 Soft and hard target amount for NeoPrep Nicklas Nordborg enhancement major Reggie v4.3 net.sf.basedb.reggie
#876 NeoPrep library registration without Caliper files Nicklas Nordborg enhancement major Reggie v4.3 net.sf.basedb.reggie
#877 Add counter for consent forms Nicklas Nordborg enhancement minor Reggie v4.3 net.sf.basedb.reggie
#878 The YellowLabel wizard display Library *.dil items instead of Library items Nicklas Nordborg defect major Reggie v4.3.1 net.sf.basedb.reggie
#880 MeLuDI v.1.4.2 bug fixes and improvements olle task major MeLuDI v1.4.3 net.sf.basedb.meludi
#842 Update to Hibernate 5 Nicklas Nordborg task blocker LabEnv v1.5 net.sf.basedb.labenv
#525 Import data from INCA olle task major Reggie v4.4 net.sf.basedb.reggie
#872 Register Reggie as a start page Nicklas Nordborg task trivial Reggie v4.4 net.sf.basedb.reggie
#879 Switch to BASE 3.8 Nicklas Nordborg task blocker Reggie v4.4 net.sf.basedb.reggie
#882 It is not possible for a user with PatientCurator role to use the "Re-create report PDFs" button in the YellowLabel wizard Nicklas Nordborg defect minor Reggie v4.4 net.sf.basedb.reggie
#883 Add support for progress reporting to the Reggie wizard API Nicklas Nordborg enhancement major Reggie v4.4 net.sf.basedb.reggie
#884 Check timeouts for SSH commands Nicklas Nordborg enhancement minor Reggie v4.4 net.sf.basedb.reggie
#885 The ProjectArchive permission checker should use smaller batches with chmod commands Nicklas Nordborg defect major Reggie v4.4 net.sf.basedb.reggie
#886 Add thousand separator to counter on Reggie start page Nicklas Nordborg enhancement trivial Reggie v4.4 net.sf.basedb.reggie
#881 Implement INCA XML to CSV converter task blocker INCA XML to CSV converter 1.0 net.sf.basedb.inca
#887 Release export wizard Nicklas Nordborg task critical Reggie v4.5 net.sf.basedb.reggie
#888 INCA statistics olle task major Reggie v4.5 net.sf.basedb.reggie
#889 Switch to BASE 3.9 Nicklas Nordborg task blocker Reggie v4.5 net.sf.basedb.reggie
#890 Remove calls to methods deprecated in BASE 3.9 Nicklas Nordborg enhancement major Reggie v4.5 net.sf.basedb.reggie
#892 Add support for enforcing YubiKey login depending on client Nicklas Nordborg enhancement major YubiKey v1.3 net.sf.basedb.yubikey
#893 Add support for using login+password+yubikey otp when logging in Nicklas Nordborg enhancement major YubiKey v1.3 net.sf.basedb.yubikey
#894 Update YubiKey JAR file Nicklas Nordborg task major YubiKey v1.3 net.sf.basedb.yubikey
#895 Switch to Java 8 and BASE 3.9 Nicklas Nordborg task major YubiKey v1.3 net.sf.basedb.yubikey
#891 Report delivery system Nicklas Nordborg task critical Reggie v4.6 net.sf.basedb.reggie
#896 INCA import should include laterality mapping column olle task minor Reggie v4.6 net.sf.basedb.reggie
#898 INCA import should create trimmed tab-delimited file with synonymized data olle task major Reggie v4.6 net.sf.basedb.reggie
#899 There is an empty line in 'cohortCase.txt' Nicklas Nordborg defect trivial Reggie v4.6 net.sf.basedb.reggie
#900 Switch to BASE 3.9.1 Nicklas Nordborg task blocker Reggie v4.6 net.sf.basedb.reggie
#901 Set multiple paths for run-archive Nicklas Nordborg enhancement major Reggie v4.6 net.sf.basedb.reggie
#902 Incorrect counter on reggie start page Nicklas Nordborg defect major Reggie v4.6 net.sf.basedb.reggie
#897 Generate SCAN-B referral forms in Reggie olle task major Reggie v4.7 net.sf.basedb.reggie
#903 The Inca import wizard is no longer experimental Nicklas Nordborg defect trivial Reggie v4.7 net.sf.basedb.reggie
#906 Create alias for Patient, Case, Specimen and Blood items for external use Nicklas Nordborg task major Reggie v4.7 net.sf.basedb.reggie
#907 Remove code that can create patient items from the follow-up blood registration wizard Nicklas Nordborg enhancement minor Reggie v4.7 net.sf.basedb.reggie
#908 Support for re-processing from lysate Nicklas Nordborg enhancement major Reggie v4.7 net.sf.basedb.reggie
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