Bash – How to run a program that has its own command line within a shell script program

bashcommand linescriptingshell-script

I need to write a shell script to automatically run a set of files through an existing program ~1000 times. The program I'm trying to run them through is accessed through command line as follows, then you load the files you want the program to use by typing in "load filetype filename" as follows:

server>./fbat

               *******************************************************
               *                                                     *
               *     *********  * * *          *       *********     *
               *     *          *     *       * *          *         *
               *     *******    *  * *       *   *         *         *
               *     *          *     *     * *** *        *         *
               *     *          *     *    *       *       *         *
               *     *          * * *     *         *      *         *
               *                                                     *
               *          Xin Xu  C1999-2009       v2.0.4Q       *
               *          Program for Population Genetics            *
               *          Harvard School of Public Health            *
               *                                                     *
               *******************************************************

>>load map leprmap.txt

read in 899 markers' info

>>load ped leprped.txt

read in: 899 markers from 16 pedigrees (338 nuclear families,1182 persons)

>>load phe phe_dbpsim2e1.txt

1 quantitative traits have been successfully read
719 persons have been phenotyped

>>trait resid

affection resid** 

>>fbat -v1 -e

(…lots of output here)

The file that will change with each run is phe_dbpsim2e1.txt, the name of which increments by one number each run. I'm able to execute the program from a script, but once the program is open, it doesn't recognize any of the commands I am trying to input through the script (i.e. load) and the program waits for me to manually input commands. Once I quit the program, all of my commands from the script show up on the screen, so it seems like the script I wrote is paused while the program is open.

Is there a way to input commands into the program once it's open without typing them in by hand?

Best Answer

If fbat insists on getting its input from the terminal and you want to automate, the solution is to use expect (or pexpect). Here is an example of an expect script which might automate your program:

#!/usr/bin/expect -f
spawn ./fbat
expect ">>"
send "load map leprmap.txt\r"
expect ">>"
send "load phe phe_dbpsim2e1.txt\r"
expect ">>"
send "trait resid\r"

Because I don't have access to fbat, the above is, of course, not tested.

To install expect on a debian-like sytem, run:

apt-get install expect

Read from a pipe, write to a file

If you want the daemon to read input produced by some arbitrary process, you need to connect that process to a pipe. Here the arbitrary process is you echoing commands, and it's going to run in a different context. So create a named pipe (often called a fifo in unix contexts).

mkfifo /var/run/daemon.fifo
</var/run/daemon.fifo /path/to/daemond --option >daemon.log

And just write commands to the pipe:

echo 'FORWARD 10' >/var/run/daemon.fifo
echo 'LEFT 72' >/var/run/daemon.fifo

This is unlikely to work as is however: there's a good chance that the daemon will exit when it sees an end of file on its standard input, which happens as soon as the first process that writes to the pipe terminates. You can use tail -f to avoid that problem.

</var/run/daemon.fifo tail -c +1 -f | {
  echo $$ >/var/run/daemon.pid
  exec /path/to/daemond --option >daemon.log
}

With some tail implementations, you may get bitten by buffering: the tail process will wait until it has amassed enough bytes to emit some output. I don't think this is solvable in the POSIX toolbox; if that's a problem, use a trivial C or Perl or Python program. As far as I can tell the tail from GNU coreutils (as found on Linux and elsewhere) is safe on this respect.

When you stop the daemon, echo >/var/run/daemon.fifo will kill the tail process.

Starting the program inside screen

Instead of invoking the daemon directly from your service manager (are you really using just SysV init, or something additional like wrapper scripts or Upstart?), invoke

screen -c daemon.screenrc -L -d -m -S daemon_name /path/to/daemond --option

Since the daemon won't be a child process of the service manager, you need to make sure to send a signal to the right process. How to do that depends on exactly how the daemon is started and by what.

It's technically possible to attach a running process to a terminal, but there's a risk you'll crash the program, so this is definitely out for a production system.

The -L option makes screen write everything that appears in its window to a file. The file name is given in daemon.screenrc with the logfile directive.

How to run the own program without specifying its path

What you are looking for is the PATH environmental variable. It tells the shell, where it needs to look for programs. You can see the current value of that variable using echo:

echo "$PATH"

Now... The best practice if you want use some new program is to install it using the package management program for your distribution. But in this case, I assume you are dealing with a program that is not delivered by any available software package. For such programs, you have two options:

Install the program system-wide, in a place where your system does not put any files installed from packages. On most systems, such "safe" folders include /usr/local/bin/ and /opt/bin/ - those should already be in your PATH. (Look inside these folders and if there are many files in them, then it is the wrong place to put your own program and you have to look at other folders listed in your PATH.)
Modify your PATH variable. This is less secure, because it defines additional folders where programs can be kept and someone might play a trick on you, putting his own program there for you to run.

You can modify the PATH variable either temporarily, using
```
export PATH="$PATH:/path/to/your/executable"
```
(mind the $PATH after =), or permanently by adding the above line to your .bashrc file (assuming you use bash).

Best Answer

Related Solutions

Shell – How to make a shell script that sends output to a process

Read from a pipe, write to a file

Starting the program inside screen

How to run the own program without specifying its path

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