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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/analyzegenes.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 September 27, 2018
7
8 Description: Generates a prokaryotic gene model (.pkm) for gene calling.
9 Input is fasta and gff files.
10 The .pkm file may be used by CallGenes.
11
12 Usage: analyzegenes.sh in=x.fa gff=x.gff out=x.pgm
13
14 File parameters:
15 in=<file> A fasta file or comma-delimited list of fasta files.
16 gff=<file> A gff file or comma-delimited list. This is optional;
17 if present, it must match the number of fasta files.
18 If absent, a fasta file 'foo.fasta' will imply the
19 presence of 'foo.gff'.
20 out=<file> Output pgm file.
21
22 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
23 "
24 }
25
26 #This block allows symlinked shellscripts to correctly set classpath.
27 pushd . > /dev/null
28 DIR="${BASH_SOURCE[0]}"
29 while [ -h "$DIR" ]; do
30 cd "$(dirname "$DIR")"
31 DIR="$(readlink "$(basename "$DIR")")"
32 done
33 cd "$(dirname "$DIR")"
34 DIR="$(pwd)/"
35 popd > /dev/null
36
37 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
38 CP="$DIR""current/"
39
40 z="-Xmx2g"
41 z2="-Xms2g"
42 set=0
43
44 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
45 usage
46 exit
47 fi
48
49 calcXmx () {
50 source "$DIR""/calcmem.sh"
51 setEnvironment
52 parseXmx "$@"
53 }
54 calcXmx "$@"
55
56 function analyze() {
57 local CMD="java $EA $EOOM $z $z2 -cp $CP prok.AnalyzeGenes $@"
58 #echo $CMD >&2
59 eval $CMD
60 }
61
62 analyze "$@"