|Version 4 (modified by 2 years ago) ( diff ),|
Updating to Reggie 4.32
Note that BASE 3.19 is required for running Reggie 4.32.
A. Updated pipeline script
singlecolumnaverager.awk script has been updated (see #1325). Install the new version at a suitable location and make sure to update reggie-config.xml with the new path.
B. 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
- ImportArchive: This should be configure to access
The same paths also need to be specified in the
reggie-config.xml file in
Also, a new entry
<step-1-import> is needed since the first Trimmomatic step is different in the import pipeline.
C. After updating Reggie
1. Change existing software items
Demuxingsoftware should be annotated with
Mergingsoftware should be annoteted with
2. Create new software items
- Create a new
Demuxingsoftware representing the bcl2fastq demuxing that is done by CMD. Annotate
ExternalRef=bcl2fastqand make it project default.
- Create a new
Mergingsoftware representing the FASTQ import variant that uses a different Trimmomatic first step. Annotate
Pipeline=RNAseqand 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.