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Full Discussion: Help with writing a script to run java commands in sequence in UNIX
Top Forums Shell Programming and Scripting Help with writing a script to run java commands in sequence in UNIX Post 302934844 by Wixaros on Wednesday 11th of February 2015 09:42:06 AM
Old 02-11-2015
Help with writing a script to run java commands in sequence in UNIX
Hi,

Brand new to these forums, and I hope that someone can help me out.

I'm trying to run the following command in UNIX
Code:
java -jar GenomeAnalysisTK.jar -T SplitSamFile -dt NONE -R reference.fa -I my.bam --outputRoot /my/path/SampleFiles/Sample_

It executes the SplitSamFile from GATK, but I want to run 3 additional commands, in a sequence. I can get them to run simultaneously but not in sequence, as I'm not able to pause the jobs (using ctrl + z) and put them in the background.

I've tried the following in my UNIX bash system (example with just two commands):
Code:
java -jar GenomeAnalysisTK.jar -T SplitSamFile -dt NONE -R reference.fa -I my1.bam --outputRoot /my/path/SampleFiles/Sample_ &; java -jar GenomeAnalysisTK.jar -T SplitSamFile -dt NONE -R reference.fa -I my2.bam --outputRoot /my/path/SampleFiles/Sample_ &

but this gives me the following error:

Code:
-bash: syntax error near unexpected token `;'

I've tried to consider doing a SH script, but can't figure out how to make the commands come in sequence rather than all starting at the same time.

Hope someone can help me out.
Last edited by Wixaros; 02-11-2015 at 11:53 AM..
 

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LEARN ABOUT SUNOS

times

times(1)							   User Commands							  times(1)

NAME

       times - shell built-in function to report time usages of the current shell

SYNOPSIS

   sh
       times

   ksh
       times

DESCRIPTION

   sh
       Print the accumulated user and system times for processes run from the shell.

   ksh
       Print the accumulated user and system times for the shell and for processes run from the shell.

       On this man page, ksh(1) commands that are preceded by one or two * (asterisks) are treated specially in the following ways:

       1.  Variable assignment lists preceding the command remain in effect when the command completes.

       2.  I/O redirections are processed after variable assignments.

       3.  Errors cause a script that contains them to abort.

       4.  Words,  following a command preceded by ** that are in the format of a variable assignment, are expanded with the same rules as a vari-
	   able assignment. This means that tilde substitution is performed after the = sign and word splitting and file name generation  are  not
	   performed.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWcsu			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       ksh(1), sh(1), time(1), attributes(5)

SunOS 5.10							    15 Apr 1994 							  times(1)
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