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Full Discussion: perl: Command works in terminal, but not in shell script
Top Forums Shell Programming and Scripting perl: Command works in terminal, but not in shell script Post 302801595 by jdilts on Thursday 2nd of May 2013 09:53:19 AM
Old 05-02-2013
perl: Command works in terminal, but not in shell script
Hi, the following command works in the terminal no problem.
Code:
samtools view -h rawlib.bam | perl -ne '{ @line = split( /\s+/ ); $match = 0; while( $line[5] =~ /(\d+)M/g ) { $match = $match + $1 } if( $match >= 80 || $_ =~ /^\@/ ) { print $_ } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=rawlib.gt80.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate; samtools index rawlib.gt80.bam

But when I plop it in a shell script and change the file names to given execution variables......
Code:
run "samtools view -h ${ANALYSIS_DIR}/${BARCODE_ID}_rawlib.bam | perl -ne '{ @line = split( /\s+/ ); $match = 0; while( $line[5] =~ /(\d+)M/g ) { $match = $match + $1 } if( $match >= 80 || $_ =~ /^\@/ ) { print $_ } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=${ANALYSIS_DIR}/${BARCODE_ID}_rawlib.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate";samtools index ${ANALYSIS_DIR}/${BARCODE_ID}_rawlib.bam

I get an error.
Code:
running: samtools view -h /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam | perl -ne '{ @line = split( /\s+/ );  = 0; while( runplugin/runlevel	""[5] =~ /(\d+)M/g ) {  =  + -j } if(  >= 80 || /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam =~ /^\@/ ) { print /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=/results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate
String found where operator expected at -e line 1, near "runlevel """
	(Do you need to predeclare runlevel?)
Bareword found where operator expected at -e line 1, near "06mar2013"
	(Missing operator before mar2013?)
Bareword found where operator expected at -e line 1, near "40p12rpt"
	(Missing operator before p12rpt?)
Bareword found where operator expected at -e line 1, near "06mar2013"
	(Missing operator before mar2013?)
Bareword found where operator expected at -e line 1, near "40p12rpt"
	(Missing operator before p12rpt?)
syntax error at -e line 1, near "; ="
syntax error at -e line 1, near "runlevel """
syntax error at -e line 1, near "( >="
syntax error at -e line 1, near "} }"
Execution of -e aborted due to compilation errors.

It looks as though the error starts occurring at
Code:
 $match = 0;

.
I've attached my code. Probably a syntax error?
launch.sh (1.6 KB) 
 

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