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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 January 21, 2020
7
8 Description: Generates synthetic PacBio reads to mimic the chimeric
9 inverted repeats from 'triangle reads', aka 'ice cream cones' -
10 reads missing one adapter.
11
12 Usage: icecreammaker.sh in=<file> out=<file> reads=100k minlen=500 maxlen=5000
13
14 Standard parameters:
15 in=<file> A reference genome fasta (optional).
16 out=<file> Synthetic read output.
17 idhist=<file> Identity histogram output.
18 overwrite=f (ow) Set to false to force the program to abort rather than
19 overwrite an existing file.
20 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
21 level; lower compression is faster.
22
23 Length parameters:
24 NOTE: "length" parameters dictate subread length (for normal reads).
25 "Movie" parameters dictate sequence length (with concatenated subreads).
26
27 minlen=500 (minlength) Minimum length of genomic sequence molecules.
28 maxlen=5000 (maxlength) Maximum length of genomic sequence molecules.
29 len= (length) Set minlen and maxlen to the same number.
30 minmovie=500 (minmov) Minimum length of movies.
31 maxmovie=40k (maxmov) Maximum length of movies.
32 movie= (mov) Set minmov and maxmov to the same number.
33
34 Ice cream parameters:
35 missingrate=0 (missing) Fraction of reads missing an adapter.
36 hiddenrate=0 (hidden) Fraction of adapters not detected.
37 bothends=f Allow missing or hiddden adapters on both ends.
38
39 Other parameters:
40 zmws (reads) Number of ZMWs to generate. There are actually
41 multiple subreads per zmw.
42 ccs=f Make CCS reads (one read per ZMW, full pass only).
43 You still need to specify the error rate.
44 gc=0.6 If a random genome is generated, use this GC fraction.
45 genomesize=10m If a random genome is generated, make it this big.
46 irrate=0.0 Add inverted repeats until this fraction of the genome
47 is inverted repeats.
48 irminlen=500 Minimum length of inverted repeats.
49 irmaxlen=5000 Maximum length of inverted repeats
50 irlen= Set minirlen and maxirlen to the same number.
51 miner=0.05 (minerrorrate) Minimum error rate.
52 maxer=0.28 (maxerrorrate) Maximum error rate.
53 er= (errorrate) Set minerrorrate and maxerrorrate.
54 NOTE: You can alternatively set minid, maxid, or id.
55
56
57 Java Parameters:
58 -Xmx This will set Java's memory usage, overriding autodetection.
59 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
60 specify 200 megs. The max is typically 85% of physical memory.
61 -eoom This flag will cause the process to exit if an out-of-memory
62 exception occurs. Requires Java 8u92+.
63 -da Disable assertions.
64
65 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
66 "
67 }
68
69 #This block allows symlinked shellscripts to correctly set classpath.
70 pushd . > /dev/null
71 DIR="${BASH_SOURCE[0]}"
72 while [ -h "$DIR" ]; do
73 cd "$(dirname "$DIR")"
74 DIR="$(readlink "$(basename "$DIR")")"
75 done
76 cd "$(dirname "$DIR")"
77 DIR="$(pwd)/"
78 popd > /dev/null
79
80 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
81 CP="$DIR""current/"
82
83 z="-Xmx2g"
84 z2="-Xms2g"
85 set=0
86
87 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
88 usage
89 exit
90 fi
91
92 calcXmx () {
93 source "$DIR""/calcmem.sh"
94 setEnvironment
95 parseXmx "$@"
96 if [[ $set == 1 ]]; then
97 return
98 fi
99 freeRam 2000m 42
100 z="-Xmx${RAM}m"
101 z2="-Xms${RAM}m"
102 }
103 calcXmx "$@"
104
105 icecreammaker() {
106 local CMD="java $EA $EOOM $z -cp $CP icecream.IceCreamMaker $@"
107 echo $CMD >&2
108 eval $CMD
109 }
110
111 icecreammaker "$@"