= Updating to Reggie 4.27 = **Note that BASE 3.16 is required for running Reggie 4.26.** == A. Before updating Reggie == === 1. Install new/updated pipeline scripts === There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk Download and install at a suitable location on the prime cluster: * `novaseq_status.sh`: Used by auto-confirmation to check status of !NovaSeq sequencing. === 2. Install R-script for the Single Sample Predictor === TODO === 3. Import annotation types that are required for storing SSP results === The [attachment:ssp_annotationtypes.xlsx] file contains definitions for annotation types required for the SSP models. Upload this file to BASE and use the batch annotation type importer to create the annotation types. It should create 16 new `SSP_*` annotation types. == B. Update Reggie == Update Reggie to version 4.27. Add the following models to the `//` section in `reggie-config.xml` (remove the `` entry that is already there). Do not forget to run the Installation wizard. {{{ Training_Run19081Genes_noNorm_SSP.PAM50subtype4Most.Fcc15_5x5foldCV.num.rules.50_21.selRules.AIMS.GS.RData Training_Run19081Genes_noNorm_SSP.subtypeMost.Fcc15_5x5foldCV.num.rules.50_24.selRules.AIMS.GS.Rdata Training_Run19081Genes_noNorm_SSP.scaled.ROR.tot.asT0.c005.Fcc15_5x5foldCV.num.rules.50_21.selRules.AIMS.GS.RData Training_Run19081Genes_noNorm_SSP.ER_v2.Fcc15_5x5foldCV.num.rules.50_19.selRules.AIMS.GS.RData Training_Run19081Genes_noNorm_SSP.PR_v2.Fcc15_5x5foldCV.num.rules.50_3.selRules.AIMS.GS.Rdata Training_Run19081Genes_noNorm_SSP.HER2.Fcc15_5x5foldCV.num.rules.50_8.selRules.AIMS.GS.RData Training_Run19081Genes_noNorm_SSP.CClusterK20_15_5x5foldCV.num.rules.50_27.selRules.AIMS.GS.Rdata Training_Run19081Genes_noNorm_SSP.iC10.mimic_5x5foldCV.num.rules.50_41.selRules.AIMS.GS.RData }}}