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