#571 |
Update Reggie to new scripting pattern (first step)
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v2.16
|
net.sf.basedb.reggie
|
#583 |
Require 'embedding date' in 'Register paraffin blocks' wizard
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.15
|
net.sf.basedb.reggie
|
#630 |
Start cufflinks
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v2.17
|
net.sf.basedb.reggie
|
#641 |
Import data from cufflinks result files
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v2.17
|
net.sf.basedb.reggie
|
#652 |
New location of BASE JAR files
|
Jari Häkkinen
|
task
|
critical
|
|
not classified
|
#656 |
FASTQ files are not always stored in the expected folder
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.16.1
|
net.sf.basedb.reggie
|
#658 |
Adjust fragment size mean and standard deviation
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v2.16.1
|
net.sf.basedb.reggie
|
#662 |
Race conditions in demux script
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.16.2
|
net.sf.basedb.reggie
|
#667 |
Library registration wizard complains about missing concentration for Stratagene
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.16.3
|
net.sf.basedb.reggie
|
#669 |
RNAQC Caliper well table import wizard should check if values are missing
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.17
|
net.sf.basedb.reggie
|
#672 |
RNA concentration normalization wizard
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v2.18
|
net.sf.basedb.reggie
|
#673 |
Register RNA QC results from BioAnalyzer runs
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v2.18
|
net.sf.basedb.reggie
|
#674 |
Generate document with report of sequencing results
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v2.18
|
net.sf.basedb.reggie
|
#697 |
Can't start alignment if there are libraries without a library plate
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.17.2
|
net.sf.basedb.reggie
|
#709 |
Depend on BASE 3.4
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v3.0
|
net.sf.basedb.reggie
|
#717 |
Auto-confirmation service
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v3.0
|
net.sf.basedb.reggie
|
#719 |
NullPointerException in extraction registration wizard
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.18.1
|
net.sf.basedb.reggie
|
#727 |
RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v2.18.2
|
net.sf.basedb.reggie
|
#729 |
Check YubiKey password before user password
|
Nicklas Nordborg
|
enhancement
|
critical
|
YubiKey v1.2
|
net.sf.basedb.yubikey
|
#740 |
Add support for reprocessing specimen
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v3.2
|
net.sf.basedb.reggie
|
#753 |
Case summary breaks if no stained histology has GoodStain
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.2.1
|
net.sf.basedb.reggie
|
#757 |
Some latest RNAQC items are not fetched in the Flagged RNA wizard
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.2.1
|
net.sf.basedb.reggie
|
#773 |
The mRNA wizard must be smarter when auto-selecting pre-normalized RNA
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v3.4
|
net.sf.basedb.reggie
|
#775 |
Histology scoring wizard does not work
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.3.1
|
net.sf.basedb.reggie
|
#776 |
An old storage box position can be re-used for new specimens
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.4
|
net.sf.basedb.reggie
|
#778 |
Can't create manual pool when there is no plate waiting
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.3.2
|
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
|
#784 |
Can't create new histology work list
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.3.3
|
net.sf.basedb.reggie
|
#785 |
Separate project archive folder for external samples
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.0
|
net.sf.basedb.reggie
|
#793 |
Implement thumbnails for PNG and JPG images
|
Nicklas Nordborg
|
task
|
critical
|
Thumbnails v1.0
|
net.sf.basedb.thumbnails
|
#809 |
Improve performance of demux+merge step
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v3.6
|
net.sf.basedb.reggie
|
#812 |
Pilot report wizard
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v3.7
|
net.sf.basedb.reggie
|
#813 |
IndexOutOfBoundsException when selecting 7 lysates in the Lab Tracking Protocol for Allprep isolation wizard
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v3.6.1
|
net.sf.basedb.reggie
|
#822 |
Fix character encoding problems with R scripts
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v3.7.1
|
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
|
#834 |
Auto-analyze when sequencing has ended
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.1
|
net.sf.basedb.reggie
|
#887 |
Release export wizard
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.5
|
net.sf.basedb.reggie
|
#891 |
Report delivery system
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.6
|
net.sf.basedb.reggie
|
#904 |
Implement an Open Grid Scheduler service extension
|
Nicklas Nordborg
|
task
|
critical
|
Open Grid Scheduler service v1.0
|
net.sf.basedb.opengrid
|
#905 |
Move Open Grid Scheduler functionality to a separate extension
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.9
|
net.sf.basedb.reggie
|
#912 |
Fix report delivery system
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.7.1
|
net.sf.basedb.reggie
|
#913 |
Implement a set of wizards for handling outtakes
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.8
|
net.sf.basedb.reggie
|
#922 |
Create an example of a custom extension point
|
Nicklas Nordborg
|
task
|
critical
|
Example code v1.8
|
net.sf.basedb.examplecode
|
#938 |
Release exporter should export files that can be imported on a different server
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.10
|
net.sf.basedb.reggie
|
#939 |
Installation wizard for Relax server
|
Nicklas Nordborg
|
task
|
critical
|
Relax v1.0
|
net.sf.basedb.relax
|
#940 |
Release importer
|
Nicklas Nordborg
|
task
|
critical
|
Relax v1.0
|
net.sf.basedb.relax
|
#941 |
Create the Relax extension
|
Nicklas Nordborg
|
task
|
critical
|
Relax v1.0
|
net.sf.basedb.relax
|
#947 |
Demux fails if all barcodes have been used
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.9.2
|
net.sf.basedb.reggie
|
#962 |
Add ReferenceDate annotation to Case
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.10
|
net.sf.basedb.reggie
|
#972 |
Fix problems with bad URLs
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.10
|
net.sf.basedb.reggie
|
#983 |
Merge the Tophat alignment and Cufflinks job to a single job
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.11
|
net.sf.basedb.reggie
|
#984 |
Remove the raw data import step for Cufflinks data
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.11
|
net.sf.basedb.reggie
|
#985 |
Re-design the gene report generator so that it can produce the report using data from the cufflinks file
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.11
|
net.sf.basedb.reggie
|
#990 |
Release exporter looks for files in incorrect directory
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.11.2
|
net.sf.basedb.reggie
|
#994 |
Level 3 exporter
|
Nicklas Nordborg
|
task
|
critical
|
Relax v1.1
|
net.sf.basedb.relax
|
#995 |
Project archive files are lacking access permission
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.11.2
|
net.sf.basedb.reggie
|
#997 |
Implement new secondary analysis pipeline
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.12
|
net.sf.basedb.reggie
|
#999 |
Release exporter need to match Histology item based on partition date
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.11.3
|
net.sf.basedb.reggie
|
#1035 |
Upgrade SSHj library
|
|
enhancement
|
critical
|
Open Grid Scheduler service v1.2
|
net.sf.basedb.opengrid
|
#1039 |
Remove BouncyCastle jar files
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.19
|
net.sf.basedb.reggie
|
#1048 |
Release importer fails if the export contain integer enumerated annotation types
|
|
defect
|
critical
|
Relax v1.3
|
net.sf.basedb.relax
|
#1053 |
The "High HET" filter in the "Flagged alignments" wizard should load more alignments
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.18
|
net.sf.basedb.reggie
|
#1063 |
Specimen tube registration tries to register a new item with the same name as an existing item
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.19.1
|
net.sf.basedb.reggie
|
#1064 |
The temporary case used for holding consent information blocks registration of the real case
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.19.1
|
net.sf.basedb.reggie
|
#1086 |
Changes needed for supporting multiple authentication managers
|
Nicklas Nordborg
|
enhancement
|
critical
|
YubiKey v1.5
|
net.sf.basedb.yubikey
|
#1087 |
Changes needed for supporting multiple authentication managers
|
Nicklas Nordborg
|
enhancement
|
critical
|
OTP login v1.2
|
net.sf.basedb.otp
|
#1091 |
New annotation types in multiple new release version
|
|
defect
|
critical
|
Relax v1.4
|
net.sf.basedb.relax
|
#1103 |
Add permission check for downloading INCA report files
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.21
|
net.sf.basedb.reggie
|
#1119 |
Re-implement TIFF to JPG conversion for Histology images using the ImageIO API
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.23
|
net.sf.basedb.reggie
|
#1133 |
Re-organize the Reggie front page
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.23
|
net.sf.basedb.reggie
|
#1160 |
Investigate changes in Picard since our last modified version
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.23
|
net.sf.basedb.reggie
|
#1190 |
SCAN-B report
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.28
|
net.sf.basedb.reggie
|
#1194 |
Import more data from MIPs file
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.23.2
|
net.sf.basedb.reggie
|
#1196 |
Incorrect specifications in the mRNA protocol
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.24
|
net.sf.basedb.reggie
|
#1200 |
Release exporter changes due to Variant calling pipeline
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.26
|
net.sf.basedb.reggie
|
#1218 |
Implement MIPs alignment
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.26
|
net.sf.basedb.reggie
|
#1227 |
Switch to BASE 3.16
|
Nicklas Nordborg
|
enhancement
|
critical
|
Reggie v4.26
|
net.sf.basedb.reggie
|
#1232 |
Add support for external sequencing
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.26
|
net.sf.basedb.reggie
|
#1233 |
Add support for importing relase data with variant calling
|
|
task
|
critical
|
Relax v1.6
|
net.sf.basedb.relax
|
#1238 |
Convert variants annotations to TEXT type
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.26.2
|
net.sf.basedb.reggie
|
#1252 |
Convert SSP score annotations to TEXT type
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.27.2
|
net.sf.basedb.reggie
|
#1254 |
Incorrect time in the follow-up blood batch importer
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.27.3
|
net.sf.basedb.reggie
|
#1267 |
Mutation signature results are assigned to incorrect annotations
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.27.5
|
net.sf.basedb.reggie
|
#1272 |
Multipe auto-confirmation steps for a single item
|
Nicklas Nordborg
|
task
|
critical
|
Reggie v4.28
|
net.sf.basedb.reggie
|
#1289 |
Exclude folders from the "Stray files" wizard
|
Nicklas Nordborg
|
defect
|
critical
|
Reggie v4.30
|
net.sf.basedb.reggie
|
#2 |
enhance group/sort command in ReplicateErrorWA
|
Johan Enell
|
enhancement
|
major
|
|
onk.lu.se
|
#3 |
Create replicates with more then 2 spots
|
Johan Enell
|
enhancement
|
major
|
|
onk.lu.se
|
#12 |
RMAExpress plug-n on mac does not free temporary files when throwing an IOException
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#13 |
RMAExpress does not exit gracefully if no configuration was available
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#14 |
RMAExpress: make 'make dist' to set the proper VERSION
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#15 |
RMAExpress: Instructions on how to update
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#21 |
Make installation from the packaged source distribution work
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#33 |
Change normsdist calculations
|
Johan Enell
|
enhancement
|
major
|
|
se.lu.onk.ztest
|
#37 |
Add box-plot output
|
Johan Enell
|
enhancement
|
major
|
|
se.lu.onk.smooth
|
#38 |
Parameterparser splits the annotations values parameter incorrect
|
Johan Enell
|
defect
|
major
|
|
onk.lu.se
|
#40 |
Create virtual bioassay containing analysis results
|
Johan Enell
|
enhancement
|
major
|
|
se.lu.onk.ztest
|
#44 |
Add information on how to compile RMAExpressConsole to the RMAExpress plug-in page
|
Jari Häkkinen
|
enhancement
|
major
|
|
se.lu.thep.affymetrix
|
#45 |
PLIER - Probe Logaritmic Intensity ERror
|
Peter Johansson
|
task
|
major
|
|
se.lu.thep.affymetrix
|
#47 |
A new release of RMAExpress was released 25 March 2007.
|
Jari Häkkinen
|
defect
|
major
|
|
se.lu.thep.affymetrix
|
#49 |
Rename wiki:onk.lu.se.ZTest to wiki:se.lu.onk.ZTest
|
Jari Häkkinen
|
task
|
major
|
|
tracpages
|