Configuration.defaults

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# Configuration.defaults - Sample Yank Configuration File              #
#                                                                      #
# Copy this file to Configuration and edit before running Install.     #
#                                                                      #
#	cp Configuration.defaults Configuration                        #
#                                                                      #
# Make sure you run Install any time you edit the Configuration file.  #
########################################################################

# Path to Global Config file
MGICONFIG_PATH  /usr/local/mgi/live/mgiconfig/
GLOBAL_CONFIG   ${MGICONFIG_PATH}web/GlobalConfig

INSTALL_DIR   /usr/local/mgi/live/seqfetch/

# umask for any files created
UMASK	026

# Temporary directory where files are created that contain the
# query sequence for BLAST, and also where DUST and RepeatMasker
# read their input files.  Also note that RepeatMasker will make
# several output files in this directory after it runs.
TMPDIR         /tmp

# Absolute path to the Yank usage log file
USAGE_LOG      ${INSTALL_DIR}logs/seqfetch_usage.log

# Absolute path to the Yank error log file
ERROR_LOG      ${INSTALL_DIR}logs/seqfetch_error.log

# Run in debug mode? (0/1)
DEBUG	0

# colon-delimited list of directories containing Python libraries, including
# the lib/python directory under this installation directory
LIBDIRS		/usr/local/mgi/live/lib/python/:/usr/local/mgi/live/seqfetch/lib/python/

# Line length for FASTA format sequences returned by tool
LINE_LENGTH	60

# Overlap length for sequences split up by GCG
OVERLAP_LENGTH	10000

# EMBOSS Server
EMBOSS_HOST  bhmgiem01:8080

# EMBOSS Server
EMBOSS_URL  http://${EMBOSS_HOST}/soaplab2/services/edit.seqret

# Directory for temporary files on local server running CGI
LOCAL_TEMP_DIR /usr/tmp

# Directory for nibFrag program
NIBFRAGDIR /usr/local/bin

# Maximum number of sequences that may be retrieved
MAX_SEQS 1000

# python formatted string representing the file format of the chromosome files
# The %s is a chromosome number, X, Y, or M 
NIB_FILE_FORMAT chr%s.nib

# default genome build identifier
GENOME_BUILD GRCm39

# default mouse strain
MOUSE_STRAIN C57BL/6J

# API key for seqfetch to use for NCBI
SEQFETCH_API_KEY c63242064df64fc21a6da8d6f963db4c6808