Pipeline configuration

The pipeline is controlled by the central configuration file config_pxn.sh. This config file contains all the information about where the pipeline inputs are, the resources that will be allocated and other PDxN specific parameters. Every individual script in the pipeline depends on the contents of this config file to run proerly. The first thing you need to do is modify the variables in the config file.

DO NOT CHANGE THE VARIABLE NAMES, just modify the file paths or other values (right hand side of the = sign).

Modifications

The following table outlines the customizable parameters of the config file:

Variable	Description	Example	Available Options
GSNAMEBASE	Base name of the gene set	genedex	genedex, MSigDBv7, MSigDBv6
DSNAME	Name of the background reference dataset	gtextoil_iBrain	gtextoil, gtextoil_iBrain, HGU133plus2
OUTDIR_NAME	Name of directory to store outputs	test_run	Custom string
COLLECTION	Optional, name of collection used to augment the custom gene set (augment mode)	"test"	Custom string
NWRK_TYPE	Optional, type of network to calculate (augment)	"unipartite"	unipartite, bipartite, uni_bipartite
CORES	Number of cores (for part 1)	10	Integer
CORES_P2	Number of cores (for part 2)	25	Integer
MAX_GENES	Largest pathway size allowed	500	Integer
MIN_GENES	Smallest pathway size allowed	20	Integer
MAX_JACQ	Max Jacquard index between two pathways	85	Integer
PCOR_OPTION	Choice of partial correlation	0	0 (yes) or 1 (no)
MIN_SAMPLES	Minimum number of samples per tissue	10	Integer