Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tadwrapper.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 67:0e9998148a16 | 69:33d812a61356 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified August 18, 2016 | |
| 7 | |
| 8 Description: Generates multiple assemblies with Tadpole | |
| 9 to estimate the optimal kmer length. | |
| 10 | |
| 11 Usage: | |
| 12 tadwrapper.sh in=reads.fq out=contigs%.fa k=31,62,93 | |
| 13 | |
| 14 Parameters: | |
| 15 out=<file> Output file name. Must contain a % symbol. | |
| 16 outfinal=<file> Optional. If set, the best assembly file | |
| 17 will be renamed to this. | |
| 18 k=31 Comma-delimited list of kmer lengths. | |
| 19 delete=f Delete assemblies before terminating. | |
| 20 quitearly=f Quit once metrics stop improving with longer kmers. | |
| 21 bisect=f Recursively assemble with the kmer midway between | |
| 22 the two best kmers until improvement halts. | |
| 23 expand=f Recursively assemble with kmers shorter or longer | |
| 24 than the current best until improvement halts. | |
| 25 | |
| 26 All other parameters are passed to Tadpole. | |
| 27 " | |
| 28 } | |
| 29 | |
| 30 #This block allows symlinked shellscripts to correctly set classpath. | |
| 31 pushd . > /dev/null | |
| 32 DIR="${BASH_SOURCE[0]}" | |
| 33 while [ -h "$DIR" ]; do | |
| 34 cd "$(dirname "$DIR")" | |
| 35 DIR="$(readlink "$(basename "$DIR")")" | |
| 36 done | |
| 37 cd "$(dirname "$DIR")" | |
| 38 DIR="$(pwd)/" | |
| 39 popd > /dev/null | |
| 40 | |
| 41 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 42 CP="$DIR""current/" | |
| 43 | |
| 44 z="-Xmx14g" | |
| 45 z2="-Xms14g" | |
| 46 set=0 | |
| 47 | |
| 48 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 49 usage | |
| 50 exit | |
| 51 fi | |
| 52 | |
| 53 calcXmx () { | |
| 54 source "$DIR""/calcmem.sh" | |
| 55 setEnvironment | |
| 56 parseXmx "$@" | |
| 57 if [[ $set == 1 ]]; then | |
| 58 return | |
| 59 fi | |
| 60 freeRam 15000m 84 | |
| 61 z="-Xmx${RAM}m" | |
| 62 z2="-Xms${RAM}m" | |
| 63 } | |
| 64 calcXmx "$@" | |
| 65 | |
| 66 tadwrapper() { | |
| 67 local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadpoleWrapper $@" | |
| 68 echo $CMD >&2 | |
| 69 eval $CMD | |
| 70 } | |
| 71 | |
| 72 tadwrapper "$@" |