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Ticket Summary Owner Type Priority Milestone Component
#841 Change required BASE version to BASE 3.7 Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#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
#846 Highlight YellowLabel specimen in sample processing wizards Nicklas Nordborg enhancement major Reggie v4.1 net.sf.basedb.reggie
#847 Highlight YellowLabel specimen in library preparation wizards Nicklas Nordborg enhancement major Reggie v4.2 net.sf.basedb.reggie
#848 Enabled/disable experimental features in reggie-config.xml Nicklas Nordborg task major Reggie v4.1 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
#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
#860 NeoPrep need other barcode variants Nicklas Nordborg defect major Reggie v4.2.1 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
#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
#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
#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
#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
#883 Add support for progress reporting to the Reggie wizard API Nicklas Nordborg enhancement major 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
#888 INCA statistics olle task major 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
#897 Generate SCAN-B referral forms in Reggie olle task major Reggie v4.7 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
#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
#906 Create alias for Patient, Case, Specimen and Blood items for external use Nicklas Nordborg task major 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
#910 The Mark extracts for retraction wizard doesn't find all items in some cases Nicklas Nordborg defect major Reggie v4.7 net.sf.basedb.reggie
#911 MeLuDI should support multiple projects olle task major MeLuDI v1.5.0 net.sf.basedb.meludi
#914 Add more columns to the blacklist Nicklas Nordborg task major INCA XML to CSV converter 1.1 net.sf.basedb.inca
#915 The AutoProcessing annotation is not reset after re-processing lysate Nicklas Nordborg defect major Reggie v4.8 net.sf.basedb.reggie
#916 The consent count report should not include all consents without date Nicklas Nordborg enhancement major Reggie v4.8 net.sf.basedb.reggie
#917 Add downloaded colum to yellow label tracking wizard Nicklas Nordborg enhancement major Reggie v4.8 net.sf.basedb.reggie
#923 Move to Java 8 and BASE 3.10 Nicklas Nordborg task major Example code v1.8 net.sf.basedb.reggie
#926 SCAN-B referral form generation improvements in Reggie olle task major Reggie v4.9 net.sf.basedb.reggie
#928 Define job subtypes and use them on Open Grid jobs Nicklas Nordborg enhancement major Reggie v4.9 net.sf.basedb.reggie
#931 The "Register sequencing started" can't register if no analysis cluster is available Nicklas Nordborg defect major Reggie v4.9 net.sf.basedb.reggie
#932 Retraction wizard should be able to handle cases that only holds a consent Nicklas Nordborg defect major Reggie v4.9 net.sf.basedb.reggie
#933 Add support for exporting files to a remote server to the Release exporter plug-in Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#934 Improve API for uploading files Nicklas Nordborg enhancement major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#935 The "Re-create report PDF" function doesn't work if raw bioassay is created after 2016-12-31 Nicklas Nordborg defect major Reggie v4.9.1 net.sf.basedb.reggie
#948 Can't create mRNA plate with External RNA or Stratagene Nicklas Nordborg defect major Reggie v4.9.2 net.sf.basedb.reggie
#949 Update SSHj and Bouncy castle Nicklas Nordborg enhancement major External files support 1.3 net.sf.basedb.xfiles
#950 New pool layouts: 1x24 and 2x24 with offset Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#953 Remove "unmapped.bam" file from Tophat results Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#954 The AddOrReplaceReadGroup step in Tophat alignment should replace SCAN-B ids with external id Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#955 fix_cufflinks_tracking_id.sh should be executed on transcripts.gtf Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#956 Add support for SHA-256 fingerprints on file servers Nicklas Nordborg enhancement major External files support 1.3 net.sf.basedb.xfiles
#957 Add support for SHA-256 fingerprints on file servers enhancement major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#958 Switch to BASE 3.11 task major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#959 Switch to BASE 3.11 Nicklas Nordborg task major External files support 1.3 net.sf.basedb.xfiles
#960 Switch to BASE 3.11 Nicklas Nordborg task major Reggie v4.10 net.sf.basedb.reggie
#963 The retraction wizard can't delete top-level data folder in project archive Nicklas Nordborg defect major Reggie v4.9.4 net.sf.basedb.reggie
#964 Mark extracts for retraction wizard should set consent=no on all cases and blood items related to the patient Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#965 Retraction destruction wizard should set consent date to today on the new case item Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#966 Monthly operation list export and INCA export should not include items with consent=no Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#968 Keep LiasonComment in some cases when destructing retracted items Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#969 Changes to Frozen tissue date import wizard Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#971 Storage box creation wizard Nicklas Nordborg task major Reggie v4.11 net.sf.basedb.reggie
#974 A project should not be required olle task major LabEnv v1.6 net.sf.basedb.labenv
#975 Clean up unused javascript code olle task major LabEnv v1.6 net.sf.basedb.labenv
#976 Running 'ant update-version' doesn't update the version number in labenv.js olle defect major LabEnv v1.6 net.sf.basedb.labenv
#977 Re-design the Lab-sensor info page olle enhancement major LabEnv v1.6 net.sf.basedb.labenv
#978 Re-design the Lab sensor alarms page olle enhancement major LabEnv v1.6 net.sf.basedb.labenv
#979 Define and import Pilot report annotations Nicklas Nordborg task major Reggie v4.11 net.sf.basedb.reggie
#980 Remove Tophat-alignment data files from release exporter Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#981 Project archive need to use subfolders per site Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#987 Cohort exporter plugin Nicklas Nordborg task major Relax v1.1 net.sf.basedb.relax
#988 New pool layout: 2x16 with offset Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#992 NotEnoughRemainingQuantity in some cases when the remaining quantity is between the soft and hard target amounts Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#993 Relative dates can be incorrect due to daylight savings time Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#996 The project archive service is running to often Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#1000 The release exporter should be able to export more raw bioassay annotations Nicklas Nordborg enhancement major Reggie v4.12 net.sf.basedb.reggie
#1001 Add HaplotypeCaller to Hisat align step Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#1003 Add support for disabling/pausing a pipeline Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#1005 External data filtering and mapping wizard Nicklas Nordborg task major Reggie v4.13 net.sf.basedb.reggie
#1006 External data filtering and mapping wizard Nicklas Nordborg task major Relax v1.1 net.sf.basedb.relax
#1007 The release exporter should sort raw bioassay by external id when the "Use external ID" options is active Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#1008 The release exporter should be able to export expression data from the cufflinks file Nicklas Nordborg enhancement major Reggie v4.14 net.sf.basedb.reggie
#1009 Genotype quality control wizard Nicklas Nordborg task major Reggie v4.15 net.sf.basedb.reggie
#1013 Not enough RNA in some cases when the remaining quantity is between soft and hard target amount Nicklas Nordborg defect major Reggie v4.14 net.sf.basedb.reggie
#1014 Add column definition for "LibPlate" to derived bioassays and raw bioassays list pages Nicklas Nordborg enhancement major Reggie v4.14 net.sf.basedb.reggie
#1015 Add masking step to Hisat pipeline Nicklas Nordborg enhancement major Reggie v4.15 net.sf.basedb.reggie
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