Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/phylip2fasta.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 October 3, 2014 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Transforms interleaved phylip to fasta. |
| jpayne@69 | 9 |
| jpayne@69 | 10 Usage: phylip2fasta.sh in=<input> out=<output> |
| jpayne@69 | 11 |
| jpayne@69 | 12 Input may be stdin or an interleaved phylip file, compressed or uncompressed. |
| jpayne@69 | 13 |
| jpayne@69 | 14 Input Parameters: |
| jpayne@69 | 15 in=<file> The input phylip file; this is the only required parameter. |
| jpayne@69 | 16 unpigz=true Decompress with pigz for faster decompression. |
| jpayne@69 | 17 |
| jpayne@69 | 18 Output Parameters: |
| jpayne@69 | 19 out=<file> Fasta output destination. |
| jpayne@69 | 20 |
| jpayne@69 | 21 Java Parameters: |
| jpayne@69 | 22 -Xmx This will set Java's memory usage, overriding autodetection. |
| jpayne@69 | 23 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. |
| jpayne@69 | 24 The max is typically 85% of physical memory. |
| jpayne@69 | 25 -eoom This flag will cause the process to exit if an out-of-memory |
| jpayne@69 | 26 exception occurs. Requires Java 8u92+. |
| jpayne@69 | 27 -da Disable assertions. |
| jpayne@69 | 28 |
| jpayne@69 | 29 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 30 " |
| jpayne@69 | 31 } |
| jpayne@69 | 32 |
| jpayne@69 | 33 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 34 pushd . > /dev/null |
| jpayne@69 | 35 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 36 while [ -h "$DIR" ]; do |
| jpayne@69 | 37 cd "$(dirname "$DIR")" |
| jpayne@69 | 38 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 39 done |
| jpayne@69 | 40 cd "$(dirname "$DIR")" |
| jpayne@69 | 41 DIR="$(pwd)/" |
| jpayne@69 | 42 popd > /dev/null |
| jpayne@69 | 43 |
| jpayne@69 | 44 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 45 CP="$DIR""current/" |
| jpayne@69 | 46 |
| jpayne@69 | 47 z="-Xmx1g" |
| jpayne@69 | 48 z2="-Xms1g" |
| jpayne@69 | 49 set=0 |
| jpayne@69 | 50 |
| jpayne@69 | 51 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 52 usage |
| jpayne@69 | 53 exit |
| jpayne@69 | 54 fi |
| jpayne@69 | 55 |
| jpayne@69 | 56 calcXmx () { |
| jpayne@69 | 57 source "$DIR""/calcmem.sh" |
| jpayne@69 | 58 setEnvironment |
| jpayne@69 | 59 parseXmx "$@" |
| jpayne@69 | 60 if [[ $set == 1 ]]; then |
| jpayne@69 | 61 return |
| jpayne@69 | 62 fi |
| jpayne@69 | 63 freeRam 800m 82 |
| jpayne@69 | 64 z="-Xmx${RAM}m" |
| jpayne@69 | 65 z2="-Xms${RAM}m" |
| jpayne@69 | 66 } |
| jpayne@69 | 67 calcXmx "$@" |
| jpayne@69 | 68 |
| jpayne@69 | 69 convert() { |
| jpayne@69 | 70 local CMD="java $EA $EOOM $z -cp $CP jgi.PhylipToFasta $@" |
| jpayne@69 | 71 echo $CMD >&2 |
| jpayne@69 | 72 eval $CMD |
| jpayne@69 | 73 } |
| jpayne@69 | 74 |
| jpayne@69 | 75 convert "$@" |