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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/synthmda.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 October 22, 2015
7
8 Description: Generates synthetic reads following an MDA-amplified single cell's coverage distribution.
9
10 Usage: synthmda.sh in=<reference> out=<reads out file>
11
12 Input may be fasta or fastq, compressed or uncompressed.
13
14 Parameters:
15 reads=12000000 Generate this many reads.
16 paired=t Generate paired reads.
17 length=150 Reads should be this long.
18 minlen=4000 Min length of MDA contig.
19 maxlen=150000 Max length of MDA contig.
20 cycles=9 Number of MDA cycles; higher is more spiky.
21 initialratio=1.3 Fraction of genome initially replicated;
22 lower is more spiky.
23 ratio=1.7 Fraction of genome replicated per cycle.
24 refout=null Write MDA'd genome to this file.
25 perfect=0 This fraction of reads will be error-free.
26 amp=200 'amp' flag sent to RandomReads (higher is more spiky).
27 build=7 Index MDA'd genome in this location.
28 prefix=null Generated reads will start with this prefix.
29 overwrite=t (ow) Set to false to force the program to abort rather
30 than overwrite an existing file.
31
32 Java Parameters:
33 -Xmx This will set Java's memory usage, overriding autodetection.
34 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
35 The max is typically 85% of physical memory.
36 -eoom This flag will cause the process to exit if an
37 out-of-memory exception occurs. Requires Java 8u92+.
38 -da Disable assertions.
39
40 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
41 "
42 }
43
44 #This block allows symlinked shellscripts to correctly set classpath.
45 pushd . > /dev/null
46 DIR="${BASH_SOURCE[0]}"
47 while [ -h "$DIR" ]; do
48 cd "$(dirname "$DIR")"
49 DIR="$(readlink "$(basename "$DIR")")"
50 done
51 cd "$(dirname "$DIR")"
52 DIR="$(pwd)/"
53 popd > /dev/null
54
55 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
56 CP="$DIR""current/"
57
58 z="-Xmx4g"
59 z2="-Xms4g"
60 set=0
61
62 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
63 usage
64 exit
65 fi
66
67 calcXmx () {
68 source "$DIR""/calcmem.sh"
69 setEnvironment
70 parseXmx "$@"
71 if [[ $set == 1 ]]; then
72 return
73 fi
74 freeRam 4000m 80
75 z="-Xmx${RAM}m"
76 z2="-Xms${RAM}m"
77 }
78 calcXmx "$@"
79
80 synthmda() {
81 local CMD="java $EA $EOOM $z -cp $CP jgi.SynthMDA $@"
82 echo $CMD >&2
83 eval $CMD
84 }
85
86 synthmda "$@"