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Batch file and perl

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Special Forums Windows & DOS: Issues & Discussions Batch file and perl
# 8  
Old 11-29-2014
New batch file with the same result:

Path to cygwin exe is the first line
path to bash.exe with path to shell in the second line.

Code:
 set PATH=C:\cygwin\bin;%PATH%
    c:\cygwin\bin\bash.exe C:\cygwin\home\cmccabe\windows_annovar.sh

Cygwin opens and closes quickly. The sh file is attached in the previous post. Any suggestions? Thank you Smilie.

I placed a pause in the script and here is the error before cygwin closes:
Code:
C:\Users\cmccabe\Desktop>set PATH=C:\cygwin\bin\cygwin.exe;C:\Windows\system32;C
:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C
:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\
OpenCL SDK\2.0\bin\x64;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Bin
n\VSShell\Common7\IDE\;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Bin
n\;C:\Program Files\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files (x86)\
Microsoft SQL Server\100\DTS\Binn\

C:\Users\cmccabe\Desktop>c:\cygwin\bin\bash.exe C:\cygwin\home\cmccabe\windows_a
nnovar.sh
Press [Enter] key to continue...

Last edited by cmccabe; 11-29-2014 at 12:08 PM..
# 9  
Old 12-01-2014
Any suggestions for why this isn't working, I am at a loss. Thank you Smilie.
# 10  
Old 12-01-2014
When I use the following batch file the menu displays, but when a selection is made cygwin closes quickly.

Code:
 @echo off

C:
chdir C:\cygwin\bin\

bash --login -c "./windows_annovar.pl"
exit 0

I attached the .pl as well. Thank you Smilie.
windows_annovar.pl (5.3 KB) 
# 11  
Old 12-01-2014
Did you try to remove the "exit" from your menu point 6, or at least put a "sleep 5" in front of it?
# 12  
Old 12-01-2014
The batch below seems to execute:

Code:
 set PATH=C:\cygwin\bin\;%PATH%
    c:\cygwin\bin\bash.exe c:\cygwin\home\cmccabe\newbatch.sh

I attached the newbatch.sh, and here is a screenshot:

Code:
  
C:\Users\cmccabe\Desktop>set PATH=C:\cygwin\bin\;C:\Windows\system32;C:\Windows;
C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program
Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK
\2.0\bin\x64;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\VSShell\
Common7\IDE\;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\;C:\Prog
ram Files\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files (x86)\Microsoft
SQL Server\100\DTS\Binn\
C:\Users\cmccabe\Desktop>c:\cygwin\bin\bash.exe c:\cygwin\home\cmccabe\newbatch.
sh
 MENU
    ==================================

         1  Match patient
         2  Sanger analysis
         3  Batch analysis
         4  Individual analysis
         5  Supplemental analysis
         6  Exit

    ==================================
         Your choice:

Why is the text before MENU appearing and how do I get rid of it or hide it? Thank you Smilie.
newbatch.sh (5.1 KB) 
# 13  
Old 12-01-2014
Looks like it's "logging" your expanded set PATH command. Did you set sth. like bash's -v option's windows equivalent?
# 14  
Old 12-01-2014
I'm not sure how to do that.

Code:
 set PATH=C:\cygwin\bin\;%PATH%
    c:\cygwin\bin\bash.exe c:\cygwin\home\cmccabe\newbatch.sh

to maybe

Code:
 set PATH=%PATH%;C:\cygwin\bin\;%PATH%
    c:\cygwin\bin\bash.exe c:\cygwin\home\cmccabe\newbatch.sh

Thank you Smilie.
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