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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/fungalrelease.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 April 24, 2019
7
8 Description: Reformats a fungal assembly for release.
9 Also creates contig and agp files.
10
11 Usage: fungalrelease.sh in=<input file> out=<output file>
12
13 I/O parameters:
14 in=<file> Input scaffolds.
15 out=<file> Output scaffolds.
16 outc=<file> Output contigs.
17 qfin=<file> Optional quality scores input.
18 qfout=<file> Optional quality scores output.
19 qfoutc=<file> Optional contig quality scores output.
20 agp=<file> Output AGP file.
21 legend=<file> Output name legend file.
22 overwrite=f (ow) Set to false to force the program to abort rather than
23 overwrite an existing file.
24
25 Processing parameters:
26 fastawrap=60 Wrap length for fasta lines.
27 tuc=t Convert sequence to upper case.
28 baniupac=t Crash on encountering a non-ACGTN base call.
29 mingap=10 Expand all gaps (Ns) to be at least this long.
30 mingapin=1 Only expand gaps that are at least this long.
31 sortcscaffolds=t Sort scaffolds descending by length.
32 sortcontigs=f Sort contigs descending by length.
33 renamescaffolds=t Rename scaffolds to 'scaffold_#'.
34 scafnum=1 Number of first scaffold.
35 renamecontigs=f Rename contigs to 'contig_#' instead of 'scafname_c#'.
36 contignum=1 Number of first contig; only used if renamecontigs=t.
37 minscaf=1 Only retain scaffolds at least this long.
38 mincontig=1 Only retain contigs at least this long.
39
40 Java Parameters:
41 -Xmx This will set Java's memory usage, overriding autodetection.
42 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
43 The max is typically 85% of physical memory.
44 -eoom This flag will cause the process to exit if an
45 out-of-memory exception occurs. Requires Java 8u92+.
46 -da Disable assertions.
47
48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
49 "
50 }
51
52 #This block allows symlinked shellscripts to correctly set classpath.
53 pushd . > /dev/null
54 DIR="${BASH_SOURCE[0]}"
55 while [ -h "$DIR" ]; do
56 cd "$(dirname "$DIR")"
57 DIR="$(readlink "$(basename "$DIR")")"
58 done
59 cd "$(dirname "$DIR")"
60 DIR="$(pwd)/"
61 popd > /dev/null
62
63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
64 CP="$DIR""current/"
65
66 z="-Xmx4g"
67 z2="-Xms4g"
68 set=0
69
70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
71 usage
72 exit
73 fi
74
75 calcXmx () {
76 source "$DIR""/calcmem.sh"
77 setEnvironment
78 parseXmx "$@"
79 if [[ $set == 1 ]]; then
80 return
81 fi
82 }
83 calcXmx "$@"
84
85 fungalrelease() {
86 local CMD="java $EOOM $EA $EOOM $z $z2 -cp $CP jgi.FungalRelease $@"
87 echo $CMD >&2
88 eval $CMD
89 }
90
91 fungalrelease "$@"