jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 19, 2019
jpayne@69: 
jpayne@69: Description:  Writes a shell script to download one genome assembly
jpayne@69: and gff per genus or species, from ncbi.  Attempts to select the best assembly
jpayne@69: on the basis of contiguity.
jpayne@69: 
jpayne@69: Usage:  fetchproks.sh <url> <outfile> <max species per genus: int> <use best: t/f>
jpayne@69: 
jpayne@69: Examples:
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/ bacteria.sh 2 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/archaea/ archaea.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/viral/ viral.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/protozoa/ protozoa.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/invertebrate/ invertebrate.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/fungi/ fungi.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/plant/ plant.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/ vertebrate_mammalian.sh 0 true
jpayne@69: fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_other/ vertebrate_other.sh 0 true
jpayne@69: 
jpayne@69: Mitochondrion, plasmid, and plastid are different and use gbff2gff.
jpayne@69: 
jpayne@69: Processing parameters:
jpayne@69: None yet!
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx1g"
jpayne@69: z2="-Xms1g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: fetchproks() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP prok.FetchProks $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: fetchproks "$@"