Entering edit mode
2.1 years ago
elham
•
0
Hi, I'm trying to install provean and use it on my local machine. I get the following error.
error: BLAST database name is missing. Please edit provean.sh file to add the name.
I am configuring provean by this command line:
./configure \
--prefix=/home/elham123456/linux/provean-1.1.5 \
PSIBLAST=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/psiblast \
BLASTDBCMD=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/blastdbcmd \
CDHIT=/home/elham123456/linux/provean-1.1.5/cd-hit/bin/cd-hit \
BLAST_DB=/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr
and it is my provean.sh file
#!/bin/bash
#
# Copyright 2012-2014 J. Craig Venter Institute
# This file is part of PROVEAN. PROVEAN is free software: you may
# redistribute it and/or modify it under the terms of the GNU General Public
# License version 3. PROVEAN is distributed in the hope that it will be
# useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details. You should have received a copy of the GNU
# General Public License along with this program. If not,
# see http://www.gnu.org/licenses/gpl.txt.
#
# Name : provean.sh
# Author : Yongwook Choi
#
##############################################
####################
# CONFIGURATION
####################
# Specify the path to database and program
#
BLAST_DB="/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr"
PSIBLAST="/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/psiblast"
CD_HIT="/home/elham123456/linux/provean-1.1.5/cd-hit/bin/cd-hit"
BLASTDBCMD="/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/blastdbcmd"
# END CONFIGURATION
####################
shopt -s -o nounset
SCRIPT="provean.sh"
SCRIPT_DIR=$(readlink -f $0)
SCRIPT_DIR=${SCRIPT_DIR%/*}
if [ -z "$BLAST_DB" ] ; then
echo "error: BLAST database name is missing. Please edit provean.sh file to add the name."
exit 1;
fi
if [ -z "$PSIBLAST" ] ; then
echo "error: psiblast path is missing. Please edit provean.sh file to add the path."
exit 1
fi
if [ -z "$CD_HIT" ] ; then
echo "error: cd-hit path is missing. Please edit provean.sh file to add the path."
exit 1
fi
if [ -z "$BLASTDBCMD" ] ; then
echo "error: blastdbcmd path is missing. Please edit provean.sh file to add the path."
exit 1
fi
QUERY=
VARIATION=
QUIET="--quiet"
SSS=
SAVE_SSS=
VERBOSE=
NUM_THREADS=
TMP_DIR=
# check getopt mode
getopt -T
if [ $? -ne 4 ] ; then
echo "error: Requires enhanced getopt, obtain new version."
exit 1;
fi
OPTSTRING="q:v:Vh"
LOPTSTRING="query:,variation:,save_supporting_set:,supporting_set:,num_threads:,tmp_dir:,verbose,help"
USAGE="PROVEAN v1.1.5
USAGE:
provean.sh [Options]
Example:
# Given a query sequence in aaa.fasta file,
# compute scores for variations in bbb.var file
provean.sh -q aaa.fasta -v bbb.var
Required arguments:
-q <string>, --query <string>
Query protein sequence filename in fasta format
-v <string>, --variation <string>
Variation filename containing a list of variations:
one entry per line in HGVS notation,
e.g.: G105C, F508del, Q49dup, Q49_P50insC, Q49_R52delinsLI
Optional arguments:
--save_supporting_set <string>
Saves supporting sequence set infomation into a given filename
--supporting_set <string>
Supporting sequence set filename saved with '--save_supporting_set' option above
(This will save time for BLAST search and clustering.)
--tmp_dir <string>
Temporary directory used to store temporary files
--num_threads <integer>
Number of threads (CPUs) to use in BLAST search
-V, --verbose
Verbosely shows the information about procedure
-h, --help
Gives this help message
"
RESULT=$(getopt -n "$SCRIPT" -o "$OPTSTRING" -l "$LOPTSTRING" -- "$@")
if [ $? -ne 0 ] ; then
# parsing error, show usage
echo "$USAGE"
exit 1
fi
eval set -- "$RESULT"
while [ true ] ; do
case "$1" in
-q|--query)
shift
QUERY="$1"
;;
-v|--variation)
shift
VARIATION="$1"
;;
-V|--verbose)
QUIET=""
;;
--supporting_set)
shift
SSS="$1"
;;
--save_supporting_set)
shift
SAVE_SSS="$1"
;;
--tmp_dir)
shift
TMP_DIR="$1"
;;
--num_threads)
shift
NUM_THREADS="$1"
;;
-h|--help)
echo "$USAGE"
exit 0
;;
--)
shift
break
;;
esac
shift
done
if [ -z "$QUERY" ] ; then
echo "error: need query sequence filename"
exit 1
fi
if [ -z "$VARIATION" ] ; then
echo "error: need variation filename"
exit 1
fi
COMMAND="$SCRIPT_DIR/provean -q $QUERY -v $VARIATION -d $BLAST_DB --psiblast $PSIBLAST --cdhit $CD_HIT --blastdbcmd $BLASTDBCMD $QUIET"
if [ -n "$SAVE_SSS" ] ; then
COMMAND="$COMMAND --save_supporting_set $SAVE_SSS"
fi
if [ -n "$SSS" ] ; then
COMMAND="$COMMAND --supporting_set $SSS"
fi
if [ -n "$TMP_DIR" ]; then
COMMAND="$COMMAND --tmp_dir $TMP_DIR"
fi
if [ -n "$NUM_THREADS" ]; then
COMMAND="$COMMAND --num_threads $NUM_THREADS"
fi
# run command
$COMMAND
STATUS=$?
exit $STATUS
now, my bash file is
but I get the same error: