Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/splitribo.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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| 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 January 22, 2020 | |
| 7 | |
| 8 Description: Splits a file of various rRNAs into one file per type | |
| 9 (16S, 18S, 5S, 23s). | |
| 10 | |
| 11 Usage: splitribo.sh in=<file,file> out=<pattern> | |
| 12 | |
| 13 Standard parameters: | |
| 14 in=<file> Input file. | |
| 15 out=<pattern> Output file pattern, such as out_#.fa. The # symbol is | |
| 16 required and will be substituted by the type name, such as | |
| 17 16S, to make out_16S.fa, for example. | |
| 18 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 19 overwrite an existing file. | |
| 20 ziplevel=9 (zl) Set to 1 (lowest) through 9 (max) to change compression | |
| 21 level; lower compression is faster. | |
| 22 | |
| 23 types=16S,18S,5S,23S,m16S,m18S,p16S | |
| 24 Align to these sequences. Fewer types is faster. m16S | |
| 25 and m18S are mitochondrial; p16S is plastid (chloroplast). | |
| 26 | |
| 27 Processing parameters: | |
| 28 minid=0.59 Ignore alignments with identity lower than this to a | |
| 29 consensus sequences. | |
| 30 refineid=0.70 Refine score by aligning to clade-specific consensus if | |
| 31 the best alignment to a universal consensus is below this. | |
| 32 | |
| 33 Java Parameters: | |
| 34 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 35 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will | |
| 36 specify 200 megs. The max is typically 85% of physical memory. | |
| 37 -eoom This flag will cause the process to exit if an out-of-memory | |
| 38 exception occurs. Requires Java 8u92+. | |
| 39 -da Disable assertions. | |
| 40 | |
| 41 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 42 " | |
| 43 } | |
| 44 | |
| 45 #This block allows symlinked shellscripts to correctly set classpath. | |
| 46 pushd . > /dev/null | |
| 47 DIR="${BASH_SOURCE[0]}" | |
| 48 while [ -h "$DIR" ]; do | |
| 49 cd "$(dirname "$DIR")" | |
| 50 DIR="$(readlink "$(basename "$DIR")")" | |
| 51 done | |
| 52 cd "$(dirname "$DIR")" | |
| 53 DIR="$(pwd)/" | |
| 54 popd > /dev/null | |
| 55 | |
| 56 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 57 CP="$DIR""current/" | |
| 58 | |
| 59 z="-Xmx4g" | |
| 60 z2="-Xms4g" | |
| 61 set=0 | |
| 62 | |
| 63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 64 usage | |
| 65 exit | |
| 66 fi | |
| 67 | |
| 68 calcXmx () { | |
| 69 source "$DIR""/calcmem.sh" | |
| 70 setEnvironment | |
| 71 parseXmx "$@" | |
| 72 if [[ $set == 1 ]]; then | |
| 73 return | |
| 74 fi | |
| 75 freeRam 4000m 42 | |
| 76 z="-Xmx${RAM}m" | |
| 77 z2="-Xms${RAM}m" | |
| 78 } | |
| 79 calcXmx "$@" | |
| 80 | |
| 81 mergeribo() { | |
| 82 local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@" | |
| 83 echo $CMD >&2 | |
| 84 eval $CMD | |
| 85 } | |
| 86 | |
| 87 mergeribo "$@" |