Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/plotgc.sh @ 69:33d812a61356
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 February 27, 2017 | |
| 7 | |
| 8 Description: Prints sequence gc content once per interval. | |
| 9 | |
| 10 Usage: plotgc.sh in=<input file> out=<output file> | |
| 11 | |
| 12 Parameters: | |
| 13 in=<file> Input file. in=stdin.fa will pipe from stdin. | |
| 14 out=<file> Output file. out=stdout will pipe to stdout. | |
| 15 interval=1000 Interval length. | |
| 16 offset=0 Position offset. For 1-based indexing use offset=1. | |
| 17 psb=t (printshortbins) Print gc content for the last bin of a contig | |
| 18 even when shorter than interval. | |
| 19 | |
| 20 Java Parameters: | |
| 21 | |
| 22 -Xmx This will set Java's memory usage, overriding automatic | |
| 23 memory detection. -Xmx20g will | |
| 24 specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 25 The max is typically 85% of physical memory. | |
| 26 -eoom This flag will cause the process to exit if an out-of-memory | |
| 27 exception occurs. Requires Java 8u92+. | |
| 28 -da Disable assertions. | |
| 29 | |
| 30 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 31 " | |
| 32 } | |
| 33 | |
| 34 #This block allows symlinked shellscripts to correctly set classpath. | |
| 35 pushd . > /dev/null | |
| 36 DIR="${BASH_SOURCE[0]}" | |
| 37 while [ -h "$DIR" ]; do | |
| 38 cd "$(dirname "$DIR")" | |
| 39 DIR="$(readlink "$(basename "$DIR")")" | |
| 40 done | |
| 41 cd "$(dirname "$DIR")" | |
| 42 DIR="$(pwd)/" | |
| 43 popd > /dev/null | |
| 44 | |
| 45 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 46 CP="$DIR""current/" | |
| 47 JNI="-Djava.library.path=""$DIR""jni/" | |
| 48 JNI="" | |
| 49 | |
| 50 z="-Xmx1g" | |
| 51 z2="-Xms1g" | |
| 52 set=0 | |
| 53 | |
| 54 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 55 usage | |
| 56 exit | |
| 57 fi | |
| 58 | |
| 59 calcXmx () { | |
| 60 source "$DIR""/calcmem.sh" | |
| 61 setEnvironment | |
| 62 parseXmx "$@" | |
| 63 if [[ $set == 1 ]]; then | |
| 64 return | |
| 65 fi | |
| 66 freeRam 1400m 42 | |
| 67 z="-Xmx${RAM}m" | |
| 68 z2="-Xms${RAM}m" | |
| 69 } | |
| 70 calcXmx "$@" | |
| 71 | |
| 72 plotgc() { | |
| 73 local CMD="java $EA $EOOM $z $z2 -cp $CP driver.PlotGC $@" | |
| 74 echo $CMD >&2 | |
| 75 eval $CMD | |
| 76 } | |
| 77 | |
| 78 plotgc "$@" |