= Updating to Reggie 4.26 = **Note that BASE 3.16 is required for running Reggie 4.26.** == A. Before updating Reggie == === 1. Install new Picard version on the prime cluster === We need Picard version 2.22.3 or higher since it fixes a problem with !NovaSeq data files and the !CheckIlluminaDirectory function. Verify that the `` setting `reggie-config.xml` is poiting to the correct installation directory and modify if needed. Picard can be downloaded from https://github.com/broadinstitute/picard/releases. === 2. 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. * `mips_functions.sh`: Used by MIPs alignment. == B. Update Reggie == Update Reggie to version 4.26 as usual. Do not forget to run the Installation wizard. == C. After updating Reggie == === 1. Upload CTG sample sheet template === Upload the `CTG_SampleSheet.xlsx` file to the `/home/SCANB/Templates` directory in BASE. === 2. Create/update library preparation protocol for external sequencing === In the **Register external sequencing** wizard, a **Library preparation** protocol must be selected. The wizard will list protocols that has been annotated with `LibPrepTarget=External`. Either create a new protocol or add the External option to an existing protocol. === 3. Import variant annotations === In the **RNA library preparation and analysis**/**Variant calling pipeline** section, run the **Import variants for existing variant call raw bioassays** wizard. This wizard will import variants that are found in some interesting genes as annotations to existing raw bioassay items and will take several minutes to run. The same functionality is included in the regular variant calling script so the wizard is not needed in the future. See #1229 for more information.