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Top Forums Shell Programming and Scripting perl: Command works in terminal, but not in shell script Post 302801725 by balajesuri on Thursday 2nd of May 2013 12:53:14 PM
Old 05-02-2013
Quote:
Originally Posted by jdilts
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"

There's a small error in your perl code. A semi-colon is missing after the while block
Code:
while ( condition ) { blah }; if ($match > ......

 

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SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-a] [-c COMMAND] [-e] [-f] [-q] [-t] [file] DESCRIPTION
Script makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. Options: -a Append the output to file or typescript, retaining the prior contents. -c COMMAND Run the COMMAND rather than an interactive shell. This makes it easy for a script to capture the output of a program that behaves differently when its stdout is not a tty. -e Return the exit code of the child process. Uses the same format as bash termination on signal termination exit code is 128+n. -f Flush output after each write. This is nice for telecooperation: One person does `mkfifo foo; script -f foo' and another can super- vise real-time what is being done using `cat foo'. -q Be quiet. -t Output timing data to standard error. This data contains two fields, separated by a space. The first field indicates how much time elapsed since the previous output. The second field indicates how many characters were output this time. This information can be used to replay typescripts with realistic typing and output delays. The script ends when the forked shell exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-d (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. Script works best with commands that do not manipulate the screen, the results are meant to emulate a hardcopy terminal. ENVIRONMENT
The following environment variable is utilized by script: SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1) (for the history mechanism), scriptreplay(1). HISTORY
The script command appeared in 3.0BSD. BUGS
Script places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. AVAILABILITY
The script command is part of the util-linux package and is available from ftp://ftp.kernel.org/pub/linux/utils/util-linux/. Linux July 30, 2000 Linux
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