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Top Forums Shell Programming and Scripting Xargs to call python executable to process multiple bam files Post 303042318 by RudiC on Saturday 21st of December 2019 09:00:10 AM
Old 12-21-2019
xargs is used to turn a stream on stdin into command line arguments / parameters. sh expects its commands on stdin. Try without xargs, like
Code:
echo "..." | sh


Or, use your .py as the xargs' command but make sure it will be interpreted by python (by defining the correct "shebang").
This User Gave Thanks to RudiC For This Post:
 

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XARGS(1)						      General Commands Manual							  XARGS(1)

NAME
xargs - construct argument list(s) and execute utility SYNOPSIS
xargs [ -t ][[ -x ] -n number ][ -s size ][ utility [ arguments... ]] DESCRIPTION
The xargs utility reads space, tab, newline and end-of-file delimited arguments from the standard input and executes the specified utility with them as arguments. The utility and any arguments specified on the command line are given to the utility upon each invocation, followed by some number of the arguments read from standard input. The utility is repeatedly executed until standard input is exhausted. Spaces, tabs and newlines may be embedded in arguments using single (`` ' '') or double (``"'') quotes or backslashes (``''). Single quotes escape all non-single quote characters, excluding newlines, up to the matching single quote. Double quotes escape all non-double quote characters, excluding newlines, up to the matching double quote. Any single character, including newlines, may be escaped by a back- slash. The options are as follows: -n number Set the maximum number of arguments taken from standard input for each invocation of the utility. An invocation of utility will use less than number standard input arguments if the number of bytes accumulated (see the s option) exceeds the specified size or there are fewer than number arguments remaining for the last invocation of utility. The current default value for number is 5000. -s size Set the maximum number of bytes for the command line length provided to utility. The sum of the length of the utility name and the arguments passed to utility (including /dev/null terminators) will be less than or equal to this number. The current default value for size is ARG_MAX - 2048. -t Echo the command to be executed to standard error immediately before it is executed. -x Force xargs to terminate immediately if a command line containing number arguments will not fit in the specified (or default) command line length. If no utility is specified, echo(1) is used. Undefined behavior may occur if utility reads from the standard input. The xargs utility exits immediately (without processing any further input) if a command line cannot be assembled, utility cannot be invoked, an invocation of the utility is terminated by a signal or an invocation of the utility exits with a value of 255. The xargs utility exits with a value of 0 if no error occurs. If utility cannot be invoked, xargs exits with a value of 127. If any other error occurs, xargs exits with a value of 1. SEE ALSO
echo(1), find(1) STANDARDS
The xargs utility is expected to be IEEE Std 1003.2("POSIX") compliant. June 6, 1993 XARGS(1)
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