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Full Discussion: Change directory shell
Top Forums Shell Programming and Scripting Change directory shell Post 302922797 by cmccabe on Tuesday 28th of October 2014 10:38:38 AM
Old 10-28-2014
Change directory shell

Code:
 #!/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 that I would like to add a change directory line to.

Code:
 cd "C:\Users\cmccabe\Desktop\annovar"

can that just be added in the line after the echo? Thanks Smilie.
 

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line(1) 						      General Commands Manual							   line(1)

NAME
line - Reads one line from standard input SYNOPSIS
line STANDARDS
Interfaces documented on this reference page conform to industry standards as follows: line: XCU5.0 Refer to the standards(5) reference page for more information about industry standards and associated tags. OPTIONS
None DESCRIPTION
The line command copies one line, up to and including a newline, from standard input and writes it to standard output. Use this command within a shell command file to read from your terminal. The line command always writes at least a newline character. NOTES
The line utility has no internationalization features and is marked LEGACY in XCU Issue 5. Use the read utility instead. EXIT STATUS
Success. End-of-File. EXAMPLES
To read a line from the keyboard and append it to a file, enter: echo 'Enter comments for the log:' echo ': c' line >>log This shell procedure displays the message: Enter comments for the log: It then reads a line of text from the keyboard and adds it to the end of the file log. The echo ': c' command displays a : (colon) prompt. See the echo command for information about the c escape sequence. SEE ALSO
Commands: echo(1), ksh(1), read(1), Bourne shell sh(1b), POSIX shell sh(1p) Functions: read(2) Standards: standards(5) line(1)
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