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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 SUSE

jpackage-utils

jpackage-utils(7)						RPM Java packaging						 jpackage-utils(7)

NAME

       jpackage-utils - Utilities, macros and other files for the JPackage Project <http://www.jpackage.org/>:

SYNOPSIS

       build-classpath
	    build the Java classpath in a portable manner

       build-jar-repository
	    build a jar repository in a portable manner

       rebuild-jar-repository
	    rebuild a jar repository in a portable manner (after a jvm change...)

       build-classpath-directory
	    build the Java classpath from a directory

       diff-jars
	    show jar content differences

       jvmjar
	    install jvm extensions

       create-jar-links
	    create custom jar links

       clean-binary-files
	    remove binary files from sources

       check-binary-files
	    check for presence of unexpected binary files

DESCRIPTION

       The JPackage Project has two primary goals:

	- To provide a coherent set of Java software packages for Linux, satisfying all quality requirements of other applications.

	- To establish an efficient and robust policy for Java software packaging and installation.
	 We  focus  on	free and open source software whenever possible. For convenience, we also provide non-free packages without the restricted
	 source code.

       Our RPMs are generic in that they should work on any RPM based Linux distribution (Mandriva, Red Hat, SuSE, others). Other packaging format
	 suggestions are welcome too.

FILES

       /use/share/java-utils/java-functions
	    shell script functions library for Java applications

       /etc/java/jpackage-release
	    string identifying the currently installed JPackage release

       /etc/java/java.conf
	    system-wide Java configuration file

       ~/.java/java.conf
	    user's Java configuration

       /etc/rpm/macros.jpackage
	    RPM macros for Java packagers and developers

SEE ALSO

   Regular Manual Pages
       build-classpath(1)
       build-classpath-directory(1)
       build-jar-repository(1)
       check-binary-files(1)
       clean-binary-files(1)
       create-jar-links(1)
       diff-jars(1)
       find-jar(1)
       jvmjar(1)
       rebuild-jar-repository(1)
       rebuild-security-providers(1)
       java.conf(5)

   Documentation
       Following files are located in your standard documentation directory

       HEADER.JPP
	    A standard header with license for spec files of JPackage Project

       clean-binary-files.txt
	    A further documentation for check-binary-files(1), clean-binary-files(1) and create-jar-links(1) commands

       httpd-javadoc.conf
	    Example JPackage javadoc configuration snippet for Apache

       jpackage-1.5-policy.xhtml
	    JPackage Java infrastructure design and packaging policy

       jpackage-utils-policy
	    JPackage packaging (naming) policy

AUTHOR

       Written by the JPackage Project

REPORTING BUGS

       Report bugs using JPackage Bugzilla (http://www.jpackage.org/bugzilla/)

jpackage-utils 1.7.5						   February 2009						 jpackage-utils(7)
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