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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tadpipe.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 18, 2019
7
8 Description: Runs TadpoleWrapper after some preprocessing,
9 to allow optimal assemblies using long kmers.
10 Only paired reads are supported.
11
12 Usage:
13 tadpipe.sh in=reads.fq out=contigs.fa
14
15
16 Parameters:
17 in=<file> Input reads.
18 in2=<file> Optional read 2, if reads are in two files.
19 out=contigs.fa Output file name.
20 temp=$TMPDIR Path to a directory for temp files.
21 delete=t Delete intermediate files.
22 gz=f Gzip intermediate files.
23
24 Other parameters can be passed to individual phases like this:
25
26 assemble_k=200,250 Set kmer lengths for assembly phase.
27 merge_strict Set the strict flag in merge phase.
28 extend_el=120 Set the left-extension distance in the extension phase.
29
30 Valid prefixes:
31
32 filter_ PhiX and contaminant filtering.
33 trim_ Adapter trimmming.
34 merge_ Paired-read merging.
35 correct_ Error correction.
36 extend_ Read extension.
37 assemble_ Final assembly.
38 "
39 }
40
41 #This block allows symlinked shellscripts to correctly set classpath.
42 pushd . > /dev/null
43 DIR="${BASH_SOURCE[0]}"
44 while [ -h "$DIR" ]; do
45 cd "$(dirname "$DIR")"
46 DIR="$(readlink "$(basename "$DIR")")"
47 done
48 cd "$(dirname "$DIR")"
49 DIR="$(pwd)/"
50 popd > /dev/null
51
52 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
53 CP="$DIR""current/"
54
55 z="-Xmx14g"
56 z2="-Xms14g"
57 set=0
58
59 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
60 usage
61 exit
62 fi
63
64 calcXmx () {
65 source "$DIR""/calcmem.sh"
66 setEnvironment
67 parseXmx "$@"
68 if [[ $set == 1 ]]; then
69 return
70 fi
71 freeRam 15000m 84
72 z="-Xmx${RAM}m"
73 z2="-Xms${RAM}m"
74 }
75 calcXmx "$@"
76
77 tadpipe() {
78 local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadPipe $@"
79 echo $CMD >&2
80 eval $CMD
81 }
82
83 tadpipe "$@"