Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes432

Apr 23, 2021, 11:40:44 AM (3 years ago)
Nicklas Nordborg

Added update notes for Reggie 4.32


  • net.sf.basedb.reggie/notes432

    v1 v1  
     1= Updating to Reggie 4.32 =
     3**Note that BASE 3.18.1 is required for running Reggie 4.32.**
     5== A. Update Reggie ==
     7Update Reggie to version 4.32 as usual. Do not forget to run the Installation wizard. This will create and fix several new annotations, etc. It will still complain about File server items that need to be manually configured:
     9  * !ImportGateway: This should be configured to access `lida1:/casa17/cmdtransfer` as the `scanb` user.
     10  * !ImportArchive: This should be configure to access `lida1:/casa17/project_archive/import_archive/` as the `scanb` user.
     12The same paths also need to be specified in the `reggie-config.xml` file in `<import-gateway>` and `<import-archive>` settings.
     14Also, a new entry `<step-1-import>` is needed since the first Trimmomatic step is different in the import pipeline.
     16== B. After updating Reggie ==
     18=== 1. Change existing software items ===
     20 * All `Demuxing` software should be annotated with `DemuxType=Picard`
     21 * All `Merging` software should be annoteted with `MergeType=Default`
     23=== 2. Create new software items ===
     25 * Create a new `Demuxing` software representing the bcl2fastq demuxing that is done by CMD. Annotate `DemuxType=bcl2fastq`, `Pipeline=RNAseq`, `ExternalRef=bcl2fastq` and make it project default.
     27 * Create a new `Merging` software representing the FASTQ import variant that uses a different Trimmomatic first step. Annotate `MergeType=Import`, `Pipeline=RNAseq` and make it project default.
     30=== 3. Create or annotate protocol items ===
     32We either need to create new protocol items or annotate existing protocol items with `ExternalRef` so that they can be referenced in imports from CMD.
     34 * Library preparation
     35 * Allprep extraction (3 variants for RNA, DNA and !FlowThrough)
     36 * Sample handling