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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/lilypad.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 13, 2019
7
8 Description: Uses mapped paired reads to generate scaffolds from contigs.
9 Designed for use with ordinary paired-end Illumina libraries.
10
11 Usage: lilypad.sh in=mapped.sam ref=contigs.fa out=scaffolds.fa
12
13 Standard parameters:
14 in=<file> Reads mapped to the reference; should be sam or bam.
15 ref=<file> Reference; may be fasta or fastq.
16 out=<file> Modified reference; should be fasta.
17 overwrite=f (ow) Set to false to force the program to abort rather than
18 overwrite an existing file.
19
20 Processing parameters:
21 gap=10 Pad gaps with a minimum of this many Ns.
22 mindepth=4 Minimum spanning read pairs to join contigs.
23 maxinsert=3000 Maximum allowed insert size for proper pairs.
24 mincontig=200 Ignore contigs under this length if there is a
25 longer alternative.
26 minwr=0.8 (minWeightRatio) Minimum fraction of outgoing edges
27 pointing to the same contig. Lower values will increase
28 continuity at a risk of misassemblies.
29 minsr=0.8 (minStrandRatio) Minimum fraction of outgoing edges
30 indicating the same orientation. Lower values will increase
31 continuity at a possible risk of inversions.
32 passes=8 More passes may increase continuity.
33 samestrandpairs=f Read pairs map to the same strand. Currently untested.
34
35 Java Parameters:
36 -Xmx This will set Java's memory usage, overriding autodetection.
37 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
38 specify 200 megs. The max is typically 85% of physical memory.
39 -eoom This flag will cause the process to exit if an out-of-memory
40 exception occurs. Requires Java 8u92+.
41 -da Disable assertions.
42
43 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
44 "
45 }
46
47 #This block allows symlinked shellscripts to correctly set classpath.
48 pushd . > /dev/null
49 DIR="${BASH_SOURCE[0]}"
50 while [ -h "$DIR" ]; do
51 cd "$(dirname "$DIR")"
52 DIR="$(readlink "$(basename "$DIR")")"
53 done
54 cd "$(dirname "$DIR")"
55 DIR="$(pwd)/"
56 popd > /dev/null
57
58 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
59 CP="$DIR""current/"
60
61 z="-Xmx4g"
62 z2="-Xms4g"
63 set=0
64
65 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
66 usage
67 exit
68 fi
69
70 calcXmx () {
71 source "$DIR""/calcmem.sh"
72 setEnvironment
73 parseXmx "$@"
74 if [[ $set == 1 ]]; then
75 return
76 fi
77 freeRam 4000m 84
78 z="-Xmx${RAM}m"
79 z2="-Xms${RAM}m"
80 }
81 calcXmx "$@"
82
83 lilypad() {
84 local CMD="java $EA $EOOM $z -cp $CP consensus.Lilypad $@"
85 echo $CMD >&2
86 eval $CMD
87 }
88
89 lilypad "$@"