Updating to Reggie 4.32

Note that BASE 3.19 is required for running Reggie 4.32.

A. Update Reggie

Update 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:

• ImportGateway: This should be configured to access lida1:/casa17/cmdtransfer as the scanb user.
• ImportArchive: This should be configure to access lida1:/casa17/project_archive/import_archive/ as the scanb user.

The same paths also need to be specified in the reggie-config.xml file in <import-gateway> and <import-archive> settings.

Also, a new entry <step-1-import> is needed since the first Trimmomatic step is different in the import pipeline.

B. After updating Reggie

1. Change existing software items

• All Demuxing software should be annotated with DemuxType=Picard
• All Merging software should be annoteted with MergeType=Default

2. Create new software items

• 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.

• 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.

3. Create or annotate protocol items

We either need to create new protocol items or annotate existing protocol items with ExternalRef so that they can be referenced in imports from CMD.

• Library preparation
• Allprep extraction (3 variants for RNA, DNA and FlowThrough)
• Sample handling

4. Fix pool aliquot names

Pool aliquots created by the external sequencing wizard have incorrect names. See #1301.