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