|Version 2 (modified by 6 years ago) ( diff ),|
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.
reggie-config.xml the following changes are required:
- In the
<hisat>sub-section should be added with the full
<path>to the Hisat executable.
<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
Create a new software and protocol item for the Hisat pipeline. They should have
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