Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbmerge-auto.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 bbmerge-auto.sh is a wrapper for BBMerge that attempts to use all available |
| jpayne@69 | 6 memory, instead of a fixed amount. This is for use with the Tadpole options |
| jpayne@69 | 7 of error-correction (ecct) and extension, which require more memory. |
| jpayne@69 | 8 For merging by overlap only, please use bbmerge.sh. If you set memory |
| jpayne@69 | 9 manually with the -Xmx flag, bbmerge.sh and bbmerge-auto.sh are equivalent. |
| jpayne@69 | 10 |
| jpayne@69 | 11 For information about usage and parameters, please run bbmerge.sh. |
| jpayne@69 | 12 " |
| jpayne@69 | 13 } |
| jpayne@69 | 14 |
| jpayne@69 | 15 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 16 pushd . > /dev/null |
| jpayne@69 | 17 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 18 while [ -h "$DIR" ]; do |
| jpayne@69 | 19 cd "$(dirname "$DIR")" |
| jpayne@69 | 20 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 21 done |
| jpayne@69 | 22 cd "$(dirname "$DIR")" |
| jpayne@69 | 23 DIR="$(pwd)/" |
| jpayne@69 | 24 popd > /dev/null |
| jpayne@69 | 25 |
| jpayne@69 | 26 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 27 CP="$DIR""current/" |
| jpayne@69 | 28 JNI="-Djava.library.path=""$DIR""jni/" |
| jpayne@69 | 29 JNI="" |
| jpayne@69 | 30 |
| jpayne@69 | 31 z="-Xmx14g" |
| jpayne@69 | 32 z2="-Xms14g" |
| jpayne@69 | 33 set=0 |
| jpayne@69 | 34 |
| jpayne@69 | 35 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 36 usage |
| jpayne@69 | 37 exit |
| jpayne@69 | 38 fi |
| jpayne@69 | 39 |
| jpayne@69 | 40 calcXmx () { |
| jpayne@69 | 41 source "$DIR""/calcmem.sh" |
| jpayne@69 | 42 setEnvironment |
| jpayne@69 | 43 parseXmx "$@" |
| jpayne@69 | 44 if [[ $set == 1 ]]; then |
| jpayne@69 | 45 return |
| jpayne@69 | 46 fi |
| jpayne@69 | 47 freeRam 15000m 84 |
| jpayne@69 | 48 z="-Xmx${RAM}m" |
| jpayne@69 | 49 z2="-Xms${RAM}m" |
| jpayne@69 | 50 } |
| jpayne@69 | 51 calcXmx "$@" |
| jpayne@69 | 52 |
| jpayne@69 | 53 function merge() { |
| jpayne@69 | 54 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBMerge $@" |
| jpayne@69 | 55 echo $CMD >&2 |
| jpayne@69 | 56 eval $CMD |
| jpayne@69 | 57 } |
| jpayne@69 | 58 |
| jpayne@69 | 59 merge "$@" |