# Lines beginning with # are comments.
# All names are case sensitive.

# The two below are sent along with requests to NCBI.
# apikey is not necessary. Scripts try to get this from
# the environment variable NCBI_API_KEY.
# Please change the email to your email address.

# apikey             changethistoyourNCBI_API_KEY
email              andrew.truman@jic.ac.uk

# Downloaded genbank files are cached here.
# nopep.sh automatically generates a gbkcache
# directory in the directory it is run from.
gbkcache            gbkcache

# Filename for the SQLite3 database.
# nopep.sh automatically generates a sqlite
# directory in the directory it is run from.
sqlite3fn           sqlite/ripp.sqlite3

# Location of prodigal-short binary
# prodigalshortbin          /usr/local/bin/prodigal-short

# Location of hmmscan binary
# hmmscanbin          /usr/local/bin/hmmscan

# Directory containing the Pfam database files.
# Should be the same as pfamdir in the nopep.sh file.
hmmdir              /home/work/pfam

# Name of the Pfam database to use.
hmmdb               Pfam-A.hmm
ripphmmdb           ripp.hmm

# Name of the Pfam data file.
# Used for reading information about models.
pfamhmmdatfn        Pfam-A.hmm.dat

# Name of the SQLite3 table where results of
# hmmer searches are stored.
pfamrestab          pfamscan

# Name of the SQLite3 table where results of
# prodigal search are stored.
prepeptab           ripper

# Directory where output genbank files are stored.
# Organism names are prefixed to the file names for
# ease of identification.
# nopep.sh automatically generates an orgnamegbk directory in the
# directory it is run from.
orgnamegbkdir       /home/mnt/orgnamegbk



# Below are some defaults (commented out) that can also
# be specified in this file by removing the hashtag.
# The names are case sensitive!

# minPPlen                   20
# maxPPlen                  120
# prodigalScoreThresh        15
# maxDistFromTE            8000
# fastaOutputLimit            3
# sameStrandReward            5
# flankLen                40000