Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/processfrag.sh @ 69:33d812a61356

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified March 15, 2016
7
8 Description: Reformats output from a script.
9 Made for generating the BBMerge paper data.
10
11 Usage: processfrags.sh <file>
12
13 Processing parameters:
14 None yet!
15
16 Java Parameters:
17 -Xmx This will set Java's memory usage, overriding autodetection.
18 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
19 specify 200 megs. The max is typically 85% of physical memory.
20 -eoom This flag will cause the process to exit if an out-of-memory
21 exception occurs. Requires Java 8u92+.
22 -da Disable assertions.
23
24 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
25 "
26 }
27
28 #This block allows symlinked shellscripts to correctly set classpath.
29 pushd . > /dev/null
30 DIR="${BASH_SOURCE[0]}"
31 while [ -h "$DIR" ]; do
32 cd "$(dirname "$DIR")"
33 DIR="$(readlink "$(basename "$DIR")")"
34 done
35 cd "$(dirname "$DIR")"
36 DIR="$(pwd)/"
37 popd > /dev/null
38
39 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
40 CP="$DIR""current/"
41
42 z="-Xmx100m"
43 z2="-Xms100m"
44 set=0
45
46 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
47 usage
48 exit
49 fi
50
51 calcXmx () {
52 source "$DIR""/calcmem.sh"
53 setEnvironment
54 parseXmx "$@"
55 }
56 calcXmx "$@"
57
58 processfrags() {
59 local CMD="java $EA $EOOM $z -cp $CP driver.ProcessFragMerging $@"
60 echo $CMD >&2
61 eval $CMD
62 }
63
64 processfrags "$@"