source: Promot/trunk/promot/scripts/sbml2mdl-runner

Last change on this file was 8369, checked in by rempel, 16 years ago

scripts for functional test of sbml import:
import and simulation of all biomodels

  • Property svn:executable set to *
File size: 1.2 KB
RevLine 
[8369]1directory=$1
2extension=$2
3#outputdir=$3 #is created
4logdir=$4
5if [ ! -d $logdir ]; then mkdir -p $logdir; fi
6logfile="sbml2mdl-runner.log"
7scriptfile="sbml2mdl-runner.sh"
8#reset scriptfile
9echo "">$scriptfile
10#reset logfile, otherwise logs will be always appended
11echo "running $0 $*">$logfile
12sbml2mdlscript=`dirname $0`/sbml2mdl
13
14for file in $directory/*$extension
15do
16    #echo "$file"
17#replace xml extension to mdl, in output dir $3
18        outputdir=$3/`basename $file $extension`
19    outfilename=$outputdir/`basename $file $extension`.mdl
20    #make directory for outfile if necessary
21#    if [ ! -d $outputdir ]; then mkdir -p $outputdir; fi
22    #echo "$outfilename"
23#replace xml extension to log, in log dir $4
24    logfilename=$4/`basename $file $extension`.log
25    #echo "$logfilename"
26#log found and generated filenames
27        echo "found: $file -> $outfilename $logfilename" >> $logfile
28        echo "$sbml2mdlscript $file $outfilename >> $logfilename" >> $logfile
29            echo "$sbml2mdlscript $file $outfilename >> $logfilename" >> $scriptfile
30#start sbml2mdl with given args (write own log)     
31#    exec $sbml2mdlscript $file $outfilename >> $logfilename#only one started (the one has errors though) 
32done
33`chmod +x $scriptfile`
34exec $scriptfile
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