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Full Discussion: Use same file selected in first bash process that has matching digits in it fot the second
Top Forums Shell Programming and Scripting Use same file selected in first bash process that has matching digits in it fot the second Post 302977927 by pilnet101 on Saturday 23rd of July 2016 03:24:37 PM
Old 07-23-2016
Sorry about that, I've amended the script slightly so it should work as expected now:

Code:
#!/bin/bash
FILESDIR=/home/cmccabe/Desktop/files
ANNOVARDIR=/home/cmccabe/Desktop/annovar

PS3="please select a file to analyze with a panel: "
select file in $(cd ${FILESDIR};ls *); do
        [[ -z ${file} ]] && printf "Pick a file" || break
done

file1=${FILESDIR}/${file}
file2=$(ls ${ANNOVARDIR}/${file%%_*}*)
printf "File 1 is: ${file1}\n"
printf "File 2 is: ${file2}\n"

It looks like basename isn't really required as you are dealing with the file names themselves straight from the select loop. Then when you create the file1 variable you append the directory in front of it.
This User Gave Thanks to pilnet101 For This Post:
cmccabe
 

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LEARN ABOUT SUSE

bashbug

BASHBUG(1)						      General Commands Manual							BASHBUG(1)

NAME

       bashbug - report a bug in bash

SYNOPSIS

       bashbug [--version] [--help] [email-address]

DESCRIPTION

       bashbug	is  a shell script to help the user compose and mail bug reports concerning bash in a standard format.	bashbug invokes the editor
       specified by the environment variable EDITOR on a temporary copy of the bug report format outline. The user must fill  in  the  appropriate
       fields  and  exit  the  editor.	 bashbug  then	mails the completed report to bug-bash@gnu.org, or email-address.  If the report cannot be
       mailed, it is saved in the file dead.bashbug in the invoking user's home directory.

       The bug report format outline consists of several sections.  The first section provides information about the  machine,	operating  system,
       the  bash  version, and the compilation environment.  The second section should be filled in with a description of the bug.  The third sec-
       tion should be a description of how to reproduce the bug.  The optional fourth section is for a proposed fix.  Fixes are encouraged.

ENVIRONMENT

       bashbug will utilize the following environment variables if they exist:

       EDITOR Specifies the preferred editor. If EDITOR is not set, bashbug defaults to emacs.

       HOME   Directory in which the failed bug report is saved if the mail fails.

       TMPDIR Directory in which to create temporary files and directories.

SEE ALSO

       bash(1)

AUTHORS

       Brian Fox, Free Software Foundation
       bfox@gnu.org

       Chet Ramey, Case Western Reserve University
       chet@po.cwru.edu

GNU Bash-4.0							   1998 July 30 							BASHBUG(1)
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