https://github.com/streptomyces/ripper
Tip revision: 44ecc7291a78ea739afe2774eb65345b190d31e6 authored by streptomyces on 01 November 2023, 12:24:35 UTC
Additions to .gitignore.
Additions to .gitignore.
Tip revision: 44ecc72
local.conf
# Lines beginning with # are comments.
# All names are case sensitive.
# Downloaded genbank files are cached here.
# ripper_run.sh automatically generates a gbkcache
# directory in the directory it is run from.
gbkcache gbkcache
# Filename for the SQLite3 database.
# ripper_run.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 ripper_run.sh file.
hmmdir 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.
# ripper_run.sh automatically generates an orgnamegbk directory in the
# directory it is run from.
orgnamegbkdir /home/mnt/orgnamegbk
blastdbdir blastdb
# 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 12500