That is a great suggestion Aia. I have been trying to make a bash to make it easier for users to use without needing much scripting, ideally none but as little as needed. Anyway, below is a start (I hope):
Code:
#!/usr/bin/perl
use strict;
use warnings;
use Switch;
my $input = '';
while ($input ne '7')
{
clear_screen();
print "type 1 for mutation match\n".
"type 2 for annovar conversion\n".
"type 3 for individual or sanger annotation\n".
"type 4 for batch or sanger annotation\n".
"type 5 for individual noonan syndrome anotation\n".
"type 6 for batch noonan syndrome annotation\n".
"type 7 to end\n";
print "Enter your choice: ";
$input = <STDIN>;
chomp($input);
switch ($input)
{
case '1'
{
$input = '';
I am not sure if that is correct or how to call a command based on the menu selection. For example, if 1 is inputed, then something like this needs to result.
Code:
printf "Enter ID : "; read id
printf "What panel: "; read panel
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
OMR=Output_Mutation_Report
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
Thank you all for the great suggestions and ideas, I have a lot to learn .
Hi all,
I'm trying to wirte a small shell script in Linux. My script has the flow like,
cmd1
cmd2
cd testdata
cmd3
After exiting the program, the CWD remains the same as where I execute the program. I need it to be changed to the latest updated directory in the program. How can I do... (1 Reply)
hi,
Iam in directory A. I run a script from there. inside the script i have a command cd B.
When i come out of the script directory is A only.
Even when i come out scrip i want the directory to be B
How to achieve (2 Replies)
I would like to have a script that would change my current working directory. However, any time I execute a 'cd' command in a script, it holds only for the life of that script -- the working directory on exit is the same as when the script was initiated. Is it possible to have the script return... (3 Replies)
I have a directory that is existing under my root dir of the FTP server. The DIR name is 'Software Patch'. I want to move in to that DIR to download some patches. But, when I issued a command 'cd SOftware Patch', the system said that it cannot find the dir 'Software'. I tried all possible ways like... (2 Replies)
I have a directory of files and each file has a random 5 digit string at the beginning that needs to be removed. Plus, there are some files that will be identically named after the 5 digit string is removed and I want those eliminated or moved.
any ideas? (17 Replies)
I have a simple shell script that prompts the user to enter a directory to navigate to.
What i want it to do and i don't know how to do this is if the directory is invalid automatically navigate to the home directory.
echo "enter a directory to navigate to:"
read directory
cd $directory... (6 Replies)
Hi,
I Installed mysql on my CentOS 6.2 Server. But when I tried to change the location of /var/lib/mysql to another directory. I can't start the mysql. Below is what I've done
yum install mysql mysql-server mysql-devel
mkdir /path/to/new/
cp -R /var/lib/mysql /path/to/new
chown -R... (1 Reply)
I am trying to do the following task :
export ENV=aaa
export ENV_PATH=$(cd /apps | ls | grep $ENV)
However, it's not working. What's the way to change to directory and search some file in that directory in single command
Please help. (2 Replies)
Hi All,
There is a code like below in my script
###############################################
###Create Directories and Sub-Directories
###############################################
dpdir=DP_FROM_${from}_TO_${to}
mkdir $dpdir
cd $dpdir
mkdir AWQM WFCONTROLLER PROVCO PRISM
... (1 Reply)
#!/bin/bash
echo -n "Enter number of sanger patients : "; read id
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
I have the above script... (7 Replies)
Discussion started by: cmccabe
7 Replies
LEARN ABOUT SUNOS
gnome-panel-preferences
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)
11-11-2014
.