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.

In reggie-config.xml the following changes are required:

• In the <programs> section, a <hisat> sub-section should be added with the full <path> to the Hisat executable.
• A <align-hisat> section with Hisat configuration parameters should be added. The configuration file shipped with Reggie should contain functional default values.

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.