Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/taxtree.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 Jan 7, 2020 | |
| 7 | |
| 8 Description: Creates tree.taxtree from names.dmp and nodes.dmp. | |
| 9 These are in taxdmp.zip available at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ | |
| 10 The taxtree file is needed for programs that can deal with taxonomy, | |
| 11 like Seal and SortByTaxa. | |
| 12 | |
| 13 Usage: taxtree.sh names.dmp nodes.dmp merged.dmp tree.taxtree.gz | |
| 14 | |
| 15 Java Parameters: | |
| 16 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 17 -Xmx20g will specify 20 gigs of RAM. The max is typically 85% of physical memory. | |
| 18 -eoom This flag will cause the process to exit if an out-of-memory | |
| 19 exception occurs. Requires Java 8u92+. | |
| 20 -da Disable assertions. | |
| 21 | |
| 22 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 23 " | |
| 24 } | |
| 25 | |
| 26 #This block allows symlinked shellscripts to correctly set classpath. | |
| 27 pushd . > /dev/null | |
| 28 DIR="${BASH_SOURCE[0]}" | |
| 29 while [ -h "$DIR" ]; do | |
| 30 cd "$(dirname "$DIR")" | |
| 31 DIR="$(readlink "$(basename "$DIR")")" | |
| 32 done | |
| 33 cd "$(dirname "$DIR")" | |
| 34 DIR="$(pwd)/" | |
| 35 popd > /dev/null | |
| 36 | |
| 37 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 38 CP="$DIR""current/" | |
| 39 JNI="-Djava.library.path=""$DIR""jni/" | |
| 40 JNI="" | |
| 41 | |
| 42 z="-Xmx2g" | |
| 43 z2="-Xms2g" | |
| 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 if [[ $set == 1 ]]; then | |
| 56 return | |
| 57 fi | |
| 58 freeRam 2000m 84 | |
| 59 z="-Xmx${RAM}m" | |
| 60 z2="-Xms${RAM}m" | |
| 61 } | |
| 62 calcXmx "$@" | |
| 63 | |
| 64 | |
| 65 taxtree() { | |
| 66 local CMD="java $EA $EOOM $z $z2 -cp $CP tax.TaxTree $@" | |
| 67 echo $CMD >&2 | |
| 68 eval $CMD | |
| 69 } | |
| 70 | |
| 71 taxtree "$@" |