Windows & DOS: Issues & Discussions

I have created a windows batch file to run a bash with perl commands in it:

Code:

 @echo off

C:
chdir C:\cygwin\bin\

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

In the pl file attached the menu opens and the user makes a selection and cygwin closes. There are error messages on the screen but it closes too quickly to see them. How can I pause the batch file and keep it from closing so I can see the messages and being troubleshooting? Thank you .

1. This is an MS-DOS question and is more appropriate in this forum.
2. I think it would be more convenient to directly run the perl program rather than wrapping it in a batch script. Not sure if you have a specific constraint for doing it this way.
3. If you do want to use it, look at the pause command.

I will move the post and look into pause. Thank you .

I have created a windows batch file to run a bash with perl commands in it:

Code:

 @echo off

C:
chdir C:\cygwin\bin\

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

In the pl file attached the menu opens and the user makes a selection and cygwin closes. There are error messages on the screen but it closes too quickly to see them. How can I pause the batch file and keep it from closing so I can see the messages and being troubleshooting? Thank you .

Merged the 2 threads...

You're going about this all wrong.
The files you have attached
are the same file. You can't just rename files and expect them to run with different interpreters.

Code:

Line 117  windows_annovar.sh

    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver ... blah blah blah)

This is calling perl table_annovar.pl to access a database (humandb) I think. Do you have all those perl files installed?? If so, perl needs to know where to find them. The full path to the folder that contains them should be in PATH as well as the full path to the perl modules.

PATH belongs in windows_annovar.sh...not this one. Actually, it belongs in the shell environment.
Get rid of this file.

Code:

windows_annovar.pl
#!/bin/bash

PATH="C:\\cygwin\\bin\perl.exe:${PATH}"
...
...

Code:

 @echo off

C:
chdir C:\cygwin\bin\

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

Cygwin opens and closes quickly. The sh file is attached and in the file there are cd commands that contain the humandb. If I run it from the command line using

Code:

 bash ~/newbatch.sh

it runs fine. Since I am using windows I altered that file a bit and would like to have a user just double click on the bat file to run the program. Thank you .