Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/idtree.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell |
| jpayne@69 | 6 Last modified July 1, 2016 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Makes a Newick tree from an identity matrix. |
| jpayne@69 | 9 Intended for use with matrices created by idmatrix.sh. |
| jpayne@69 | 10 |
| jpayne@69 | 11 Usage: idtree.sh in=<input file> out=<output file> |
| jpayne@69 | 12 |
| jpayne@69 | 13 Standard parameters: |
| jpayne@69 | 14 in=<file> Identity matrix in TSV format. |
| jpayne@69 | 15 out=<file> Newick tree output. |
| jpayne@69 | 16 overwrite=f (ow) Set to false to force the program to abort rather than |
| jpayne@69 | 17 overwrite an existing file. |
| jpayne@69 | 18 |
| jpayne@69 | 19 Processing parameters: |
| jpayne@69 | 20 None yet! |
| jpayne@69 | 21 |
| jpayne@69 | 22 Java Parameters: |
| jpayne@69 | 23 -Xmx This will set Java's memory usage, overriding autodetection. |
| jpayne@69 | 24 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will |
| jpayne@69 | 25 specify 200 megs. The max is typically 85% of physical memory. |
| jpayne@69 | 26 -eoom This flag will cause the process to exit if an out-of-memory |
| jpayne@69 | 27 exception occurs. Requires Java 8u92+. |
| jpayne@69 | 28 -da Disable assertions. |
| jpayne@69 | 29 |
| jpayne@69 | 30 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 31 " |
| jpayne@69 | 32 } |
| jpayne@69 | 33 |
| jpayne@69 | 34 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 35 pushd . > /dev/null |
| jpayne@69 | 36 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 37 while [ -h "$DIR" ]; do |
| jpayne@69 | 38 cd "$(dirname "$DIR")" |
| jpayne@69 | 39 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 40 done |
| jpayne@69 | 41 cd "$(dirname "$DIR")" |
| jpayne@69 | 42 DIR="$(pwd)/" |
| jpayne@69 | 43 popd > /dev/null |
| jpayne@69 | 44 |
| jpayne@69 | 45 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 46 CP="$DIR""current/" |
| jpayne@69 | 47 |
| jpayne@69 | 48 z="-Xmx800m" |
| jpayne@69 | 49 z2="-Xms800m" |
| jpayne@69 | 50 set=0 |
| jpayne@69 | 51 |
| jpayne@69 | 52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 53 usage |
| jpayne@69 | 54 exit |
| jpayne@69 | 55 fi |
| jpayne@69 | 56 |
| jpayne@69 | 57 calcXmx () { |
| jpayne@69 | 58 source "$DIR""/calcmem.sh" |
| jpayne@69 | 59 setEnvironment |
| jpayne@69 | 60 parseXmx "$@" |
| jpayne@69 | 61 if [[ $set == 1 ]]; then |
| jpayne@69 | 62 return |
| jpayne@69 | 63 fi |
| jpayne@69 | 64 freeRam 800m 84 |
| jpayne@69 | 65 z="-Xmx${RAM}m" |
| jpayne@69 | 66 z2="-Xms${RAM}m" |
| jpayne@69 | 67 } |
| jpayne@69 | 68 calcXmx "$@" |
| jpayne@69 | 69 |
| jpayne@69 | 70 idtree() { |
| jpayne@69 | 71 local CMD="java $EA $EOOM $z -cp $CP tax.IDTree $@" |
| jpayne@69 | 72 echo $CMD >&2 |
| jpayne@69 | 73 eval $CMD |
| jpayne@69 | 74 } |
| jpayne@69 | 75 |
| jpayne@69 | 76 idtree "$@" |