Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/comparessu.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified December 4, 2019 | |
| 7 | |
| 8 Description: Aligns SSUs to each other and reports identity. | |
| 9 This requires sequences annotated with a taxID in their header. | |
| 10 | |
| 11 Usage: comparessu.sh in=<input file> out=<output file> | |
| 12 | |
| 13 Input may be fasta or fastq, compressed or uncompressed. | |
| 14 | |
| 15 Standard parameters: | |
| 16 in=<file> Input sequences. | |
| 17 out=<file> Output data. | |
| 18 t= Set the number of threads; default is logical processors. | |
| 19 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 20 overwrite an existing file. | |
| 21 showspeed=t (ss) Set to 'f' to suppress display of processing speed. | |
| 22 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression | |
| 23 level; lower compression is faster. | |
| 24 reads=-1 If positive, quit after this many sequences. | |
| 25 | |
| 26 Processing parameters: | |
| 27 ata=f Do an all-to-all comparison. Otherwise, each sequence will | |
| 28 only be compared to one other randomly-selected sequence | |
| 29 per taxonomic level. | |
| 30 minlen=0 Ignore sequences shorter than this. | |
| 31 maxlen=BIG Ignore sequences longer than this. | |
| 32 maxns=-1 If positive, ignore sequences with more than this many Ns. | |
| 33 | |
| 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 comparessu() { | |
| 84 local CMD="java $EA $EOOM $z -cp $CP sketch.CompareSSU $@" | |
| 85 echo $CMD >&2 | |
| 86 eval $CMD | |
| 87 } | |
| 88 | |
| 89 comparessu "$@" |