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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/makecontaminatedgenomes.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 29, 2017
7
8 Description: Generates synthetic contaminated partial genomes from clean genomes.
9 Output is formatted as (prefix)_bases1_fname1_bases2_fname2_counter_(suffix).
10
11 Usage: makecontaminatedgenomes.sh in=<file> out=<pattern>
12
13 I/O parameters:
14 in=<file> A file containing one input file path per line.
15 out=<pattern> A file name containing a # symbol (or other regex).
16 The regex will be replaced by source filenames.
17
18 Processing Parameters:
19 count=1 Number of output files to make.
20 seed=-1 RNG seed; negative for a random seed.
21 exp1=1 Exponent for genome 1 size fraction.
22 exp2=1 Exponent for genome 2 size fraction.
23 subrate=0 Rate to add substitutions to new genomes (0-1).
24 indelrate=0 Rate to add substitutions to new genomes (0-1).
25 regex=# Use this substitution regex for replacement.
26 delimiter=_ Use this delimiter in the new file names.
27
28 Java Parameters:
29 -Xmx This will set Java's memory usage, overriding autodetection.
30 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
31 The max is typically 85% of physical memory.
32 -eoom This flag will cause the process to exit if an out-of-memory
33 exception occurs. Requires Java 8u92+.
34 -da Disable assertions.
35
36 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
37 "
38 }
39
40 #This block allows symlinked shellscripts to correctly set classpath.
41 pushd . > /dev/null
42 DIR="${BASH_SOURCE[0]}"
43 while [ -h "$DIR" ]; do
44 cd "$(dirname "$DIR")"
45 DIR="$(readlink "$(basename "$DIR")")"
46 done
47 cd "$(dirname "$DIR")"
48 DIR="$(pwd)/"
49 popd > /dev/null
50
51 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
52 CP="$DIR""current/"
53
54 z="-Xmx4g"
55 z2="-Xms4g"
56 set=0
57
58 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
59 usage
60 exit
61 fi
62
63 calcXmx () {
64 source "$DIR""/calcmem.sh"
65 setEnvironment
66 parseXmx "$@"
67 if [[ $set == 1 ]]; then
68 return
69 fi
70 freeRam 4000m 42
71 z="-Xmx${RAM}m"
72 }
73 calcXmx "$@"
74
75 makecontaminatedgenomes() {
76 local CMD="java $EA $EOOM $z -cp $CP jgi.MakeContaminatedGenomes $@"
77 echo $CMD >&2
78 eval $CMD
79 }
80
81 makecontaminatedgenomes "$@"