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Old 05-28-2014, 02:41 AM   #48
Junior Member
Location: London

Join Date: Feb 2014
Posts: 3
Default Escaping spaces using the shell script

Hi Brian,
I can't seem to work out how to pass a filepath with spaces in it to BBMap using the shell script. Nothing that I normally would use seems to work...


 ~/bbmap/ ref="../Reference\ genome/myref.fasta" build=2 in1=./Reads1.fastq.gz in2=./Reads2.fastq.gz out=./mapped.sam
Yields the error

Exception in thread "main" java.lang.RuntimeException: Unknown parameter: genome/myref.fasta
Is there a way to pass a string with escaped spaces to bbmap using the shell script or do I need to call bbmap directly?

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