shell script not running in php

[raman]

I have embedded a shell script within a php script.

 

The shell script runs correctly when I run it from the shell, however when I run it from the browser, only the first part of it runs while the second part does not. multiplets.o is a binary executable of c++ program. Can someone suggest? My machine is a Redhat eneterprise linux and php is 5.3.1

 

seqfile=$1;

#first part
cp $seqfile $seqfile.test;
perl -pi -e "s/\t/\n/" $seqfile.test;
perl -pi -e "s/>/>0/" $seqfile.test;
perl fast_betteramcomph.pl $seqfile.test $seqfile.aac;

  #second part
./multiplets.o $seqfile.test $seqfile.mp > waste;
cut -d ' ' -f 1-20 $seqfile.mp > $seqfile.mpc;
perl -pi -e "s/$/ /" $seqfile.mpc;
rm -rf $seqfile.mp;

[jl5501]

I would suggest making the paths to the files, full system path names. if they are not already. I would agree that it is odd that perl is finding the files in your first half, but I would certainly give that a try.

 

It is certainly going to be the case that the default path setup is going to be different for the user running the shellscript from the shell command line, then it is for the user running apache.

[raman]

I added the full system paths, but that did not help in any way.

[jl5501]

ok so 2 things.

 

1) I assume that your script does have the #!/bin/bash or whatever for the shell interpreter you wish to run.

 

2) Does your own executable have the appropriate execute permissions for the user running apache?

[raman]

I have tried both the ways, with and without #!/bin/bash. It does not make any difference

 

 

Also even when I set the permission as 777, it does not help.

[jl5501]

Then I would suggest that your executable is expecting something in its environment that it is not finding. I think you are going to have to put some extensive debug output in your executable, starting with a simple, 'yes I have started'

[raman]

Yes you are right

The problem is with this line,

./multiplets.o $seqfile.test $seqfile.mp > waste;

 

when I put this as ./multiplets.o $seqfile.test $seqfile.mp , the script runs correctly, but the problem is that the useless information that I was directing to the file waste also appears on the browser, my output files is only $seqfile.mp, i need only that one.

 

 

can you suggest what should be done about this ?

[jl5501]

Ok so is the waste output on stdout or stderr?

 

If you do not want to keep this output I would suggest >/dev/null 2>&1

 

or >/tmp/waste 2>&1  if you do want to keep it

[raman]

thank you, this helps.

 

But I don't understand the meaning of

/dev/null 2>&1  and

/tmp/waste 2>&1

[jl5501]

With any command that runs, there are 2 output streams, stdout and stderr.

 

>  redirects stdout as you have done

2> redirects stderr

 

>2&1 says redirect stderr to same place as stdout

[raman]

with stderr, I understand that it means the error messages.

 

However, there is no error as such in this case. I don't understand why it works for me.