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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/comparegff.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified August 12, 2019
7
8 Description: Compares CDS, rRNA, and tRNA lines in gff files.
9
10 Usage: comparegff.sh in=<input gff> ref=<reference gff>
11
12 Standard parameters:
13 in=<file> Query gff.
14 ref=<file> Reference gff.
15
16 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
17 "
18 }
19
20 #This block allows symlinked shellscripts to correctly set classpath.
21 pushd . > /dev/null
22 DIR="${BASH_SOURCE[0]}"
23 while [ -h "$DIR" ]; do
24 cd "$(dirname "$DIR")"
25 DIR="$(readlink "$(basename "$DIR")")"
26 done
27 cd "$(dirname "$DIR")"
28 DIR="$(pwd)/"
29 popd > /dev/null
30
31 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
32 CP="$DIR""current/"
33
34 z="-Xmx1g"
35 z2="-Xms1g"
36 set=0
37
38 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
39 usage
40 exit
41 fi
42
43 calcXmx () {
44 source "$DIR""/calcmem.sh"
45 setEnvironment
46 parseXmx "$@"
47 if [[ $set == 1 ]]; then
48 return
49 fi
50 freeRam 1000m 42
51 z="-Xmx${RAM}m"
52 z2="-Xms${RAM}m"
53 }
54 calcXmx "$@"
55
56 comparegff() {
57 local CMD="java $EA $EOOM $z -cp $CP gff.CompareGff $@"
58 echo $CMD >&2
59 eval $CMD
60 }
61
62 comparegff "$@"