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Full Discussion: Combine shell files
Top Forums Shell Programming and Scripting Combine shell files Post 302924361 by sea on Saturday 8th of November 2014 11:00:17 AM
Old 11-08-2014
show_func expects a single string, therefor you must pass 'anything' you pass, as a single string.

What is the (terminal) output of (by itself):
Code:
perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf (index id 0) :: $entry

And for the case itself, you need to embrace that commabd by : "$( CMD )" (including the quotes!), where CMD is the complete perl command, when called by itself returns exactly what you want.

Its not Windows Smilie
It linux, so try either one of:
  • $HOME/Desktop/annovar
  • /home/annovar/Desktop/annovar
  • /home/$USER/Desktop/annovar
  • $XDG_DESKTOP_DIR/annovar

Hope this helps
 

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gnome-panel-preferences(1)					   User Commands					gnome-panel-preferences(1)

NAME
gnome-panel-preferences - configure the behavior of panels SYNOPSIS
gnome-panel-preferences [gnome-std-options] DESCRIPTION
The Panel preference tool enables you to configure the behavior of all of your panels. OPTIONS
The following options are supported: gnome-std-optionStandard options available for use with most GNOME applications. See gnome-std-options(5). EXAMPLES
Example 1: Launching the Panel preference tool example% gnome-panel-preferences EXIT STATUS
The following exit values are returned: 0 Application exited successfully >0 Application exited with failure FILES
The following files are used by this application: /usr/bin/gnome-panel-preExecutable for Panel preferences tool ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWgnome-panel | +-----------------------------+-----------------------------+ |Interface stability |External | +-----------------------------+-----------------------------+ SEE ALSO
Preference Tools Manual Latest version of the GNOME Desktop User Guide for your platform. gnome-panel(1), gnome-std-options(5) NOTES
Written by Glynn Foster, Sun Microsystems Inc., 2003. SunOS 5.10 2 Oct 2003 gnome-panel-preferences(1)
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