Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/textfile.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| 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: Displays contents of a text file. |
| jpayne@69 | 9 Start line and stop line are zero-based. Start is inclusive, |
| jpayne@69 | 10 stop is exclusive. |
| jpayne@69 | 11 |
| jpayne@69 | 12 Usage: textfile.sh <file> <start line> <stop line> |
| jpayne@69 | 13 |
| jpayne@69 | 14 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| 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 set=0 |
| jpayne@69 | 32 |
| jpayne@69 | 33 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 34 usage |
| jpayne@69 | 35 exit |
| jpayne@69 | 36 fi |
| jpayne@69 | 37 |
| jpayne@69 | 38 calcXmx () { |
| jpayne@69 | 39 source "$DIR""/calcmem.sh" |
| jpayne@69 | 40 setEnvironment |
| jpayne@69 | 41 parseXmx "$@" |
| jpayne@69 | 42 } |
| jpayne@69 | 43 calcXmx "$@" |
| jpayne@69 | 44 |
| jpayne@69 | 45 function tf() { |
| jpayne@69 | 46 local CMD="java $EA $EOOM -Xmx120m -cp $CP fileIO.TextFile $@" |
| jpayne@69 | 47 echo $CMD >&2 |
| jpayne@69 | 48 eval $CMD |
| jpayne@69 | 49 } |
| jpayne@69 | 50 |
| jpayne@69 | 51 tf "$@" |