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Ticket Summary Owner Type Priority Milestone Component
#1217 DoNotUse flags and comments should be copied to new child items Nicklas Nordborg enhancement minor Reggie v4.25 net.sf.basedb.reggie
#1219 Start demux wizard for MIPs should be a separate wizard Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1220 Auto-analyze in the MIPs pipeline should start the demux Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1221 Display more information in the Variant summary dialog Nicklas Nordborg enhancement minor Reggie v4.25 net.sf.basedb.reggie
#1222 Remove the G5 distance calculations from the variant calling script Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1223 Implement an option to skip labels for the Histology specimen in the partitioning wizard Nicklas Nordborg enhancement trivial Reggie v4.25 net.sf.basedb.reggie
#1224 The RNAseq library preperation wizard display protocols from other pipelines Nicklas Nordborg defect major Reggie v4.25 net.sf.basedb.reggie
#1225 Update databases used in variant calling pipeline Nicklas Nordborg enhancement blocker Reggie v4.25 net.sf.basedb.reggie
#363 Add 'install' target to ant build script Nicklas Nordborg enhancement minor Illumina package v1.8 net.sf.basedb.illumina
#126 Illumina SNP ... files are now supported (by the BASEcore) in the BASE analysis tree Nicklas Nordborg enhancement major Illumina package v1.x net.sf.basedb.illumina
#196 Illumina methylation arrays ... Nicklas Nordborg defect major Illumina package v1.x net.sf.basedb.illumina
#1156 Switch to Java 11 and BASE 3.15 olle task major LabEnv v1.7 net.sf.basedb.labenv
#911 MeLuDI should support multiple projects olle task major MeLuDI v1.5.0 net.sf.basedb.meludi
#118 Create qQuantile normalizer (aka cubic-spline normalizer) Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#120 Create a normalization plug-in package. Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#161 (net.sf.basedb.normalizers) Automatic download of BASE API Martin Svensson enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#166 (net.sf.basedb.normalizers) Automatic progression of version to source code using ant Martin Svensson defect major Normalization package v1.1 net.sf.basedb.normalizers
#168 MD5 sum should be automatically generated for a package Martin Svensson task major Normalization package v1.1 net.sf.basedb.normalizers
#176 Create release document Martin Svensson task major Normalization package v1.1 net.sf.basedb.normalizers
#177 Add information about how to upgrade the normalization package. Martin Svensson task major Normalization package v1.1 net.sf.basedb.normalizers
#184 qQuantileNormalizer should update progress bar Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#186 qQuantileNormalizer method storeResult must be reimplemented Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#187 qQuantileNormalizer should allow user to select the normaliztion reference assay set Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#190 net.sf.basedb.normalizers: Add target that tries to build qQN if requested Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#191 net.sf.basedb.normalizers: qQN should support standard options ... Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#195 net.sf.basedb.normalizers: Normalizers should ask user for how to calculate averages Martin Svensson enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#197 net.sf.basedb.normalizers: Add abort functionaly to qQuantileNormalizers Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#206 net.sf.basedb.normalizers: Make qQuantileNormalization handle missing values Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#208 Revert changeset:1045 when yat bug http://dev.thep.lu.se/yat/ticket/535 is fixed Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#228 net.sf.basedb.normalizers: Normalizers should use ask BASE whether data is logged or not olle Request major Normalization package v1.1 net.sf.basedb.normalizers
#247 net.sf.basedb.normalizers: qQuantileNormalization crashes when normalizing filtered bioassay sets Jari Häkkinen defect major Normalization package v1.1 net.sf.basedb.examples.extensions
#280 Plug-in should suggest better job names Nicklas Nordborg enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#331 Updates required for BASE 3 Nicklas Nordborg task major Normalization package v1.1 net.sf.basedb.normalizers
#541 net.sf.basedb.normalizers: Normalizers should store normalized data in proper base olle Request major Normalization package v1.1 net.sf.basedb.normalizers
#551 Add 'install' target to normalizers build script Martin Svensson enhancement minor Normalization package v1.1 net.sf.basedb.normalizers
#552 PluginUtilities-0.2.jar is in incorrect location Martin Svensson defect critical Normalization package v1.1 net.sf.basedb.normalizers
#183 Change result storage of qQuantilNormalizer when BASE bioassay set export is refactored Jari Häkkinen enhancement major Normalization package v1.2 net.sf.basedb.normalizers
#927 Set cluster node on jobs Nicklas Nordborg enhancement minor Reggie v4.x net.sf.basedb.reggie
#1170 The private-key file of a file-server is ignored in the installation servlet Nicklas Nordborg defect minor Relax v1.6 net.sf.basedb.relax
#52 Add educational material and use cases. Jari Häkkinen task trivial se.lu.thep.wenni 0.7 se.lu.thep.wenni
#53 update INSTALL Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#54 update README Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#55 update ChangeLog Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#60 explain how to run wenni (base1 version) against a base_devkit Peter Johansson task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#63 make distcheck should work Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#64 configure does not find basefile.h Jari Häkkinen defect minor se.lu.thep.wenni 0.7 se.lu.thep.wenni
#145 GPL3 for WeNNI Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#146 Change references to lev.thep.lu.se to something more appropriate Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#148 BASE1 configuration: execname should be set automatically during build Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#152 Setting bindir in configure.ac destroys make distcheck Jari Häkkinen defect major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#154 wenni compiling WeNNI.java requires -encoding option to the compiler Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#156 Compilation fails in base2 test phase of 'make maintainer-check' Peter Johansson defect major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#216 Setup source code repository for GenePattern integration Nicklas Nordborg task blocker ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#217 GCT exporter Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#221 Configure GenePattern server Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#222 Utility for transfering file between BASE and a GenePattern server Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#223 Add target in build.xml for downloading required GenePattern jar files Nicklas Nordborg task major ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#224 Add a "Test" button on the GenePattern 'edit server' page Nicklas Nordborg enhancement major ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#34 move base.css Johan Enell task trivial ZZ Other tickets se.lu.onk.ztest
#77 Update information about webservice defect major ZZ Other tickets tracpages
#79 Center on assay (se.lu.onk.Center) olle task major ZZ Other tickets se.lu.onk series plug-ins
#84 Change parameter in ReplicateError (se.lu.onk.ReplicateError) olle enhancement major ZZ Other tickets se.lu.onk series plug-ins
#88 extra values pass through Jari Häkkinen enhancement major ZZ Other tickets se.lu.onk series plug-ins
#97 Remove Plier support from se.lu.thep.affymetrix Jari Häkkinen task major ZZ Other tickets se.lu.thep.affymetrix
#130 Base1PluginExecuter/ReplicateError: errors are not catched properly (se.lu.onk.ReplicateError) Jari Häkkinen defect major ZZ Other tickets se.lu.onk series plug-ins
#159 Create a se.lu.onk.VirtualArray module Jari Häkkinen task major ZZ Other tickets se.lu.onk series plug-ins
#181 Add MeV+R as a BASE extension? Jari Häkkinen task major ZZ Other tickets not classified
#255 link to APT plug-in times out Jari Häkkinen defect trivial ZZ Other tickets tracpages
#259 Apply patch provided in the BASE dev list to Tab2MageExporter Jari Häkkinen Request major ZZ Other tickets not classified
#296 VirtualArray plug-in can't be installed Jari Häkkinen defect major ZZ Other tickets se.lu.onk series plug-ins
#497 Center (se.lu.onk.Center) median calculation is flawed and should be replaced olle defect major ZZ Other tickets se.lu.onk series plug-ins
#1 Reformat plug-ins archive/download page to look like the rest of the trac environment. Jari Häkkinen task minor tracpages
#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
#41 Add data to output: sign flag, sign specific rank Jari Häkkinen enhancement minor se.lu.onk series plug-ins
#99 The tagging system of the repository should be changed Jari Häkkinen enhancement major tracpages
#115 MeV launch returns a 'jsp' extension not a 'jnlp' Nicklas Nordborg defect major net.sf.basedb.mev
#123 Update BasePlug-ins' firstpage Martin Svensson defect major tracpages
#125 MeV ... files are now supported (by the BASEcore) in the BASE analysis tree Nicklas Nordborg enhancement major net.sf.basedb.mev
#128 Warning when ftp-config.xml is missing Nicklas Nordborg enhancement major net.sf.basedb.ftp
#129 ReplicateError: Create a se.lu.onk.ReplicateError module Jari Häkkinen task major se.lu.onk series plug-ins
#131 se.lu.onk.BaseFile should be its own package Jari Häkkinen task major se.lu.onk series plug-ins
#132 ReplicateError: In witihn assays only one position of accepted replicate pairs are kept Jari Häkkinen defect critical se.lu.onk series plug-ins
#133 ReplicateError: The plug-in adds new entries to the stdout.txt for reporters that had null values in stdin.txt Jari Häkkinen enhancement major onk.lu.se
#134 BaseFile: public void resetDataPosition(BASEFileSection section) positions the file pointer one line too far Jari Häkkinen defect major onk.lu.se
#135 ReplicateError: deprecated functionality is used, get rid of it Jari Häkkinen task major se.lu.onk series plug-ins
#136 ReplicateError: Make version info to propagate automatically during ant package Jari Häkkinen defect major se.lu.onk series plug-ins
#137 Create a se.lu.onk.MergeBioAssay module Jari Häkkinen defect major se.lu.onk series plug-ins
#139 ReplciateError: A few data files are created that are always deleted with the `run` script. Jari Häkkinen enhancement major se.lu.onk series plug-ins
#149 Error: The query has already been executed (Illumina detection P-value calculation) Nicklas Nordborg defect major net.sf.basedb.illumina
#155 New error handling option for duplicated features when creating array design from a bgx-file Nicklas Nordborg enhancement minor net.sf.basedb.illumina
#157 Create a se.lu.onk.Center module Jari Häkkinen defect major se.lu.onk series plug-ins
#207 Illumina DASL arrays Nicklas Nordborg enhancement major net.sf.basedb.illumina
#236 Reporter import of Illumina BGX file fails on section [controls] Nicklas Nordborg defect major net.sf.basedb.illumina
#270 lev.thep.lu.se website down? Jari Häkkinen defect major not classified
#320 reggie 1.4 (and 1.3): cannot save if no PADCase is entered in some cases Jari Häkkinen defect critical net.sf.basedb.reggie
#393 Change default value for protocol in "RNA quality control - create aliquots" wizard step 2 Jari Häkkinen Request major net.sf.basedb.reggie
#490 Histology scoring lab protocols Nicklas Nordborg task minor net.sf.basedb.reggie
#652 New location of BASE JAR files Jari Häkkinen task critical not classified
#4 Spike Lowess Johan Enell task major onk.lu.se
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