Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/analyzegenes.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 September 27, 2018 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Generates a prokaryotic gene model (.pkm) for gene calling. |
| jpayne@69 | 9 Input is fasta and gff files. |
| jpayne@69 | 10 The .pkm file may be used by CallGenes. |
| jpayne@69 | 11 |
| jpayne@69 | 12 Usage: analyzegenes.sh in=x.fa gff=x.gff out=x.pgm |
| jpayne@69 | 13 |
| jpayne@69 | 14 File parameters: |
| jpayne@69 | 15 in=<file> A fasta file or comma-delimited list of fasta files. |
| jpayne@69 | 16 gff=<file> A gff file or comma-delimited list. This is optional; |
| jpayne@69 | 17 if present, it must match the number of fasta files. |
| jpayne@69 | 18 If absent, a fasta file 'foo.fasta' will imply the |
| jpayne@69 | 19 presence of 'foo.gff'. |
| jpayne@69 | 20 out=<file> Output pgm file. |
| jpayne@69 | 21 |
| jpayne@69 | 22 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 23 " |
| jpayne@69 | 24 } |
| jpayne@69 | 25 |
| jpayne@69 | 26 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 27 pushd . > /dev/null |
| jpayne@69 | 28 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 29 while [ -h "$DIR" ]; do |
| jpayne@69 | 30 cd "$(dirname "$DIR")" |
| jpayne@69 | 31 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 32 done |
| jpayne@69 | 33 cd "$(dirname "$DIR")" |
| jpayne@69 | 34 DIR="$(pwd)/" |
| jpayne@69 | 35 popd > /dev/null |
| jpayne@69 | 36 |
| jpayne@69 | 37 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 38 CP="$DIR""current/" |
| jpayne@69 | 39 |
| jpayne@69 | 40 z="-Xmx2g" |
| jpayne@69 | 41 z2="-Xms2g" |
| jpayne@69 | 42 set=0 |
| jpayne@69 | 43 |
| jpayne@69 | 44 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 45 usage |
| jpayne@69 | 46 exit |
| jpayne@69 | 47 fi |
| jpayne@69 | 48 |
| jpayne@69 | 49 calcXmx () { |
| jpayne@69 | 50 source "$DIR""/calcmem.sh" |
| jpayne@69 | 51 setEnvironment |
| jpayne@69 | 52 parseXmx "$@" |
| jpayne@69 | 53 } |
| jpayne@69 | 54 calcXmx "$@" |
| jpayne@69 | 55 |
| jpayne@69 | 56 function analyze() { |
| jpayne@69 | 57 local CMD="java $EA $EOOM $z $z2 -cp $CP prok.AnalyzeGenes $@" |
| jpayne@69 | 58 #echo $CMD >&2 |
| jpayne@69 | 59 eval $CMD |
| jpayne@69 | 60 } |
| jpayne@69 | 61 |
| jpayne@69 | 62 analyze "$@" |