csp2: CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/vcf2gff.sh annotate

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d

rev	line source
jpayne@69	1 #!/bin/bash
jpayne@69	2
jpayne@69	3 usage(){
jpayne@69	4 echo "
jpayne@69	5 Written by Brian Bushnell
jpayne@69	6 Last modified August 13, 2019
jpayne@69	7
jpayne@69	8 Description: Generates a GFF3 from a VCF.
jpayne@69	9
jpayne@69	10 Usage: vcf2gff.sh in=<vcf file> out=<gff file>
jpayne@69	11
jpayne@69	12 Parameters:
jpayne@69	13 in=<file> Input VCF file.
jpayne@69	14 out=<file> Output GFF file.
jpayne@69	15 "
jpayne@69	16 }
jpayne@69	17
jpayne@69	18 #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69	19 pushd . > /dev/null
jpayne@69	20 DIR="${BASH_SOURCE[0]}"
jpayne@69	21 while [ -h "$DIR" ]; do
jpayne@69	22 cd "$(dirname "$DIR")"
jpayne@69	23 DIR="$(readlink "$(basename "$DIR")")"
jpayne@69	24 done
jpayne@69	25 cd "$(dirname "$DIR")"
jpayne@69	26 DIR="$(pwd)/"
jpayne@69	27 popd > /dev/null
jpayne@69	28
jpayne@69	29 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69	30 CP="$DIR""current/"
jpayne@69	31
jpayne@69	32 z="-Xmx200m"
jpayne@69	33 set=0
jpayne@69	34
jpayne@69	35 if [ -z "$1" ] \|\| [[ $1 == -h ]] \|\| [[ $1 == --help ]]; then
jpayne@69	36 usage
jpayne@69	37 exit
jpayne@69	38 fi
jpayne@69	39
jpayne@69	40 calcXmx () {
jpayne@69	41 source "$DIR""/calcmem.sh"
jpayne@69	42 setEnvironment
jpayne@69	43 parseXmx "$@"
jpayne@69	44 }
jpayne@69	45 calcXmx "$@"
jpayne@69	46
jpayne@69	47 gff() {
jpayne@69	48 local CMD="java $EA $EOOM $z -cp $CP gff.GffLine $@"
jpayne@69	49 # echo $CMD >&2
jpayne@69	50 eval $CMD
jpayne@69	51 }
jpayne@69	52
jpayne@69	53 gff "$@"

Mercurial > repos > rliterman > csp2