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Getopt #114

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Getopt #114

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56cc736
Implement getopt for run_e2e_ver.sh
Mar 3, 2022
6971cf1
Implement getopt for run_pyrosetta_ver.sh
Mar 3, 2022
b372ea6
Add -d to Usage in help output
Mar 3, 2022
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58 changes: 53 additions & 5 deletions run_e2e_ver.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,65 @@ unset __conda_setup
# <<< conda initialize <<<
############################################################

#############
# help output
#############

function print_usage {
cat <<EOF

Usage: run_e2e_ver.sh -f <input fasta> [-w <working dir>][-c <cpus>][-m <mem>][-d <db path>]

-f, --fasta Path to fasta input
-w, --wd Path to working directory (default: your current dir)
-c, --cpus CPU cores (default: 8)
-m, --mem Memory in Gigabytes (default: 64)
-d, --db Database directory (default: pdb100_2021Mar03/pdb100_2021Mar03 in script dir)

EOF
exit 2
}

################
# default values
################

SCRIPT=`realpath -s $0`
export PIPEDIR=`dirname $SCRIPT`

WDIR=$(pwd)
CPU="8" # number of CPUs to use
MEM="64" # max memory (in GB)
DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"

##################
# argument parsing
##################

PARSED_ARGUMENTS=$(getopt -a -n run_e2e_ver.sh -o f:w:c:m:d: --long fasta:,wdir:,cpus:,mem:,db: -- "$@")
if [ $? != 0 ]; then
print_usage
fi

# Inputs:
IN="$1" # input.fasta
WDIR=`realpath -s $2` # working folder
eval set -- "$PARSED_ARGUMENTS"
while :
do
case "$1" in
-f | --fasta) IN="$2" ; shift 2 ;;
-w | --wdir) WDIR="$2" ; shift 2 ;;
-c | --cpus) CPU="$2" ; shift 2 ;;
-m | --mem) MEM="$2" ; shift 2 ;;
-d | --db) DB="$2" ; shift 2;;
-h | --help) print_usage ;;
# -- means the end of the args; drop this and break out of the while loop
--) shift; break ;;
*) print_usage ;;
esac
done

if [ -z "$IN" ]; then
echo -e "\n-f|--fasta is a required option"
print_usage
fi

LEN=`tail -n1 $IN | wc -m`

Expand Down Expand Up @@ -51,7 +100,6 @@ fi
############################################################
# 3. search for templates
############################################################
DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"
if [ ! -s $WDIR/t000_.hhr ]
then
echo "Running hhsearch"
Expand Down
58 changes: 53 additions & 5 deletions run_pyrosetta_ver.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,65 @@ unset __conda_setup
# <<< conda initialize <<<
############################################################

#############
# help output
#############

function print_usage {
cat <<EOF

Usage: run_e2e_ver.sh -f <input fasta> [-w <working dir>][-c <cpus>][-m <mem>][-d <db path>]

-f, --fasta Path to fasta input
-w, --wd Path to working directory (default: your current dir)
-c, --cpus CPU cores (default: 8)
-m, --mem Memory in Gigabytes (default: 64)
-d, --db Database directory (default: pdb100_2021Mar03/pdb100_2021Mar03 in script dir)

EOF
exit 2
}

################
# default values
################

SCRIPT=`realpath -s $0`
export PIPEDIR=`dirname $SCRIPT`

WDIR=$(pwd)
CPU="8" # number of CPUs to use
MEM="64" # max memory (in GB)
DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"

##################
# argument parsing
##################

# Inputs:
IN="$1" # input.fasta
WDIR=`realpath -s $2` # working folder
PARSED_ARGUMENTS=$(getopt -a -n run_e2e_ver.sh -o f:w:c:m:d: --long fasta:,wdir:,cpus:,mem:,db: -- "$@")
if [ $? != 0 ]; then
print_usage
fi

eval set -- "$PARSED_ARGUMENTS"
while :
do
case "$1" in
-f | --fasta) IN="$2" ; shift 2 ;;
-w | --wdir) WDIR="$2" ; shift 2 ;;
-c | --cpus) CPU="$2" ; shift 2 ;;
-m | --mem) MEM="$2" ; shift 2 ;;
-d | --db) DB="$2" ; shift 2;;
-h | --help) print_usage ;;
# -- means the end of the args; drop this and break out of the while loop
--) shift; break ;;
*) print_usage ;;
esac
done

if [ -z "$IN" ]; then
echo -e "\n-f|--fasta is a required option"
print_usage
fi

LEN=`tail -n1 $IN | wc -m`

Expand Down Expand Up @@ -51,7 +100,6 @@ fi
############################################################
# 3. search for templates
############################################################
DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"
if [ ! -s $WDIR/t000_.hhr ]
then
echo "Running hhsearch"
Expand Down