csp2: CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/grademerge.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 February 17, 2015
jpayne@69	7
jpayne@69	8 Description: Grades correctness of merging synthetic reads with headers
jpayne@69	9 generated by RandomReads and re-headered by RenameReads.
jpayne@69	10
jpayne@69	11 Usage: grademerge.sh in=<file>
jpayne@69	12
jpayne@69	13 Parameters:
jpayne@69	14 in=<file> Specify the input file, or 'stdin'.
jpayne@69	15
jpayne@69	16 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69	17 "
jpayne@69	18 }
jpayne@69	19
jpayne@69	20 #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69	21 pushd . > /dev/null
jpayne@69	22 DIR="${BASH_SOURCE[0]}"
jpayne@69	23 while [ -h "$DIR" ]; do
jpayne@69	24 cd "$(dirname "$DIR")"
jpayne@69	25 DIR="$(readlink "$(basename "$DIR")")"
jpayne@69	26 done
jpayne@69	27 cd "$(dirname "$DIR")"
jpayne@69	28 DIR="$(pwd)/"
jpayne@69	29 popd > /dev/null
jpayne@69	30
jpayne@69	31 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69	32 CP="$DIR""current/"
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 function grademerge() {
jpayne@69	41 local CMD="java $EA $EOOM -Xmx200m -cp $CP jgi.GradeMergedReads $@"
jpayne@69	42 # echo $CMD >&2
jpayne@69	43 eval $CMD
jpayne@69	44 }
jpayne@69	45
jpayne@69	46 grademerge "$@"

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