comparison pal_finder_wrapper.sh @ 3:e1a14ed7a9d6 draft

Updated to version 0.02.04.4 (new pal_filter script)

2:b6ccc7dd7b02

: ${PALFINDER_SCRIPT_DIR:=/usr/bin}
: ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04}
: ${PRIMER3_CORE_EXE:=primer3_core}
#
# Filter script is in the same directory as this script
PALFINDER_FILTER=$(dirname $0)/pal_finder_filter_and_assembly.py
if [ ! -f $PALFINDER_FILTER ] ; then
    echo No $PALFINDER_FILTER script >&2
    exit 1
fi
#

#
# Collect command line arguments
if [ $# -lt 2 ] ; then
  echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
  echo "       $0 --454    FASTA    MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
  exit
fi
if [ "$1" == "--454" ] ; then
    PLATFORM="454"
    FNA=$2
else

fi
if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then
    /bin/mv PAL_summary.filtered $FILTERED_MICROSATS
fi
if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then
    assembly=${fastq_r1%.*}_pal_finder_assembly_output.txt
    if [ -f "$assembly" ] ; then
	/bin/mv $assembly "$OUTPUT_ASSEMBLY"
    fi
fi
if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
    /bin/mv config.txt $OUTPUT_CONFIG_FILE
fi

3:e1a14ed7a9d6

: ${PALFINDER_SCRIPT_DIR:=/usr/bin}
: ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04}
: ${PRIMER3_CORE_EXE:=primer3_core}
#
# Filter script is in the same directory as this script
PALFINDER_FILTER=$(dirname $0)/pal_filter.py
if [ ! -f $PALFINDER_FILTER ] ; then
    echo No $PALFINDER_FILTER script >&2
    exit 1
fi
#

#
# Collect command line arguments
if [ $# -lt 2 ] ; then
  echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
  echo "       $0 --454    FASTA    MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
  exits
fi
if [ "$1" == "--454" ] ; then
    PLATFORM="454"
    FNA=$2
else

fi
if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then
    /bin/mv PAL_summary.filtered $FILTERED_MICROSATS
fi
if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then
    assembly=${fastq_r1%.*}_pal_filter_assembly_output.txt
    if [ -f "$assembly" ] ; then
	/bin/mv $assembly "$OUTPUT_ASSEMBLY"
    else
	echo ERROR no assembly output found >&2
	exit 1
    fi
fi
if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
    /bin/mv config.txt $OUTPUT_CONFIG_FILE
fi