4 wcd inside stackPACK

This chapter written by Peter van Heusden

Electric Genetics' stackPACK is a widely-used software suite used for expression variance analysis and transcript reconstruction.

By default, stackPACK uses d2_cluster as the clustering tool in its analysis pipeline. To incorporate wcd into stackPACK follow these steps: \

1. Install wcd as described in See Installing wcd. If you wish to use wcd from the stackPACK web user interface, you need to ensure that wcd, wcd_wrapper.sh and comp2ext.pl are runnable by the web server user.
2. Edit the /etc/stackpack file. Find the section labelled [d2_cluster] and changed the line reading executable= to refer to the location of the wcd_wrapper.sh script.

Please note that at present, you cannot do 'add' clustering in stackPACK using wcd.