= Updating to Reggie 4.12 =

=== New Hisat pipeline for secondary analysis ===

'''Do not update to Reggie 4.12 if there are items waiting in the ''Start Tophat and Cufflinks'' wizard!! '''

Due to changes in the flow control those items will disappear from the list.

=== New annotation on alignment software and protocols ===

A new annotation type, `AlignmentType` has been added. Find existing software and protocols with `Type=Alignment` and set the `AlignmentType` annotation to `Tophat`.

Create a new software and protocol item for the Hisat pipeline. They should have `Type=Alignment` and `AlignmentType=Hisat`. Keep the `Add as project default` checkbox checked and the `Replace existing default` unchecked.

=== Update the pipeline scripts ===

Install the latest pipeline scripts. The `alignment_statistics.sh` script has been updated with support for Hisat output files. Download the script from http://baseplugins.thep.lu.se/browser/other/pipeline/trunk and save it on the computation cluster in the location specified by the `<pipeline-scripts><path>` setting in `reggie-config.xml`.