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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/unzip.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 April 25, 2019
7
8 Description: Compresses or decompresses files based on extensions.
9 This only exists because the syntax and default behavior of many
10 compression utilities is unintuitive; it is just a wrapper, and
11 relies on existing executables in the command line (pigz, lbzip, etc.)
12 Does not delete the input file.
13 Does not untar files.
14
15 Usage: unzip.sh in=<file> out=<file>
16
17 Parameters:
18 in=<file> Input file.
19 out=<file> Output file for good reads.
20 zl= Set the compression level; 0-9 or 11.
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="-Xmx80m"
41 set=0
42
43 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
44 usage
45 exit
46 fi
47
48 calcXmx () {
49 source "$DIR""/calcmem.sh"
50 setEnvironment
51 parseXmx "$@"
52 }
53 calcXmx "$@"
54
55 unzip() {
56 local CMD="java $EA $EOOM $z -cp $CP jgi.Unzip $@"
57 # echo $CMD >&2
58 eval $CMD
59 }
60
61 unzip "$@"