# see http://discover.nci.nih.gov/gominer/gocommand.jsp for details of field specifications

# REQUIRED FIELDS:
# NOTE, YOU MAY NEED TO EDIT THESE TO POINT TO THE LOCATION WHERE YOU HAVE DATA AND SCRIPTS INSTALLED IN YOUR ENVIRONMENT
DATA = ../data
SCRIPTS = ../scripts
TOTALFILE = total.txt
LIST = PICK32.list

# OPTIONAL FIELDS:
# DATASOURCE = all
DATASOURCE = UniProt
ENHANCED = true
DBXREF = false
SYNONYM = false
ORGANISM = 9606
# human = 9606; mouse = 10090; rat = 10116; drosophila = 7227; c elegans = 6239; s. cerevisiae = 4932; a thaliania = 3702
# others: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy

# REASONABLE DEFAULT SETTINGS THAT YOU PROBABLY DON'T NEED TO CHANGE
RANDOMS = 100
THRESHOLD = 0.1
DEBUG = 2
TIMESERIESTHRESHOLD = 0.1

# FIELDS THAT NEED TO BE SET ONLY IF USING LOCAL GO DATABASE SERVER:
USER = deploy
PASSWORD = selectonly
DATABASE = jdbc:mysql://discover.nci.nih.gov:1521/GEEVS
DRIVER = com.mysql.jdbc.Driver

# CONFIGURATION CONTROL - PLATFORM DEPENDENT STUFF PROBABLY OK ASIS
# GREPDIR location of the version of grep that supports the -f option
GREPDIR = /usr/bin/

# TOGGLE FOR TF BINDING SITES OUTPUT - SLOWS DOWN PROGRAM IF TURNED ON
TF = 1

# TOGGLE FOR CIMs
# 0 = no CIMs (do not run CIM3.sh)
# 1 = run CIM3.sh (do not run xin-pass1.sh or xin-pass2.sh)
# 2 = run CIM3.sh and xin-pass1.sh and xin-pass2.sh
CIM = 1

# READONLY: DO NOT CHANGE THESE FOR THE TIME BEING
GO = biological_process

ROOTCATEGORY = GO:0008150

LOGFILENAME = HTGM.DEBUG

STATUSFILENAME = RETURNCODE