I would like to put my variables inside my passthru,
$cut1 =DNAseq1
$cut2 = DNAseq2
I have already checked this topic but didn't find how to proceed
echo passthru('sudo docker run my_docker bash -c "-check "' .$cut1.'" "'.$cut2);
but nothing is displayed on the screen but when I wrote directly the DNAseq1:
echo passthru('sudo docker run my_docker bash -c "-check ATCG "'.$cut );
It works....but only when I wrote one variable not for 2 So what is the problem ??
Try this:
echo passthru("sudo docker run my_docker bash -c '/home/prg/soap -check $cut1 $cut2'");
I've used double quotes around the argument to passthru() so I can substitute variables more clearly.
Related
I hope you can help me.
I am dealing with a problem that I cannot solve. This is my issue. I am trying to exec a bash script through PHP. I tried with the method
exec()
with 3 arguments, arg1, arg2, and arg3.
php code
<?php exec("./randomScript.sh arg1 arg2 arg3"); ?>
randomScript.sh
.... # random code which exploits the three arguments -> executed normally..
.... # random code which exploits the three arguments -> executed normally..
./secondScript.sh $arg1 $arg2 $arg3 #<- this is the script that is not running (is not even started).
I have tried to change the permission (I've got full permission), change the way I call the randomScript.sh (through absolute path), but nothing occurred. Besides, I tried with:
shell_exec()
method, but nothing changed. Of course, if I run the secondScript.sh via terminal everything works fine.
I cannot understand which is the problem. Could you please help me?
Thanks in advance.
In the inner shell, the arguments are not called like that (because it is invoked by the shell, not by PHP).
./secondScript.sh "$1" "$2" "$3"
or just
./secondScript.sh $*
At this stage, just remember that spaces, quotes, and dollar signs in the arguments you pass must be avoided at all costs (the solution is escaping them, but how to do it exactly is tricky).
You also might want to do instead:
$ret = shell_exec("./randomScript.sh 'arg1' 'arg2' 'arg3' 2>&1");
so that in $ret you might find error messages and output from the inner shell.
You should escape your string command before passing it in exec function, i think it may help you
Escapeshellcmd()
...
$escaped_command = escapeshellcmd("./randomScript.sh arg1 arg2 arg3");
exec($escaped_command);
...
Escapeshellarg()
For system command, i recommand using system
...
$escaped_command = escapeshellarg("./randomScript.sh arg1 arg2 arg3");
system($escaped_command);
...
You also need to make sure that your PHP code does not change working dir, and both shell scripts have execute permissions, and filesystems allows to exec files on it.
I would avoid exec("./script $arg ...");, I would rather specify the interpreter to use and full path to the script like exec("sh /home/user/project/script.sh $arg ...");
In my php file, this is how i run a bash script file.
$run=popen("/var/www/html/work/bashfile.sh","r");
and inside bashfile.sh i have something like this
#! /bin/bash
cd /var/www/html/work/prepare
./runfile 0.3 180 username
This code works perfect by producing pictures in order username1.jpg, username2.jpg
But when i try to do the same thin by passing variable to the bash script using php it does nor work and this is how i was writing the code
In my php file
$vari="name1";
$run=popen("/var/www/html/work/bashfile2.sh $vari","r");
and inside my bashfile2.sh i do
#! /bin/bash
$vari=$1
cd /var/www/html/work/prepare
./runfile 0.3 180 $vari
But this is not working. Please any idea how to work things around to end up getting the results of the first code
popen() is interpreting your variable as a part of the string you send. Try using {} to enclose your variable when using them directly in strings.
$vari = "name1";
$run = popen("/var/www/html/work/bashfile2.sh {$vari}","r");
I have a script that need to run from a terminal or a command prompt. I'm using PHP. GetOpt is the function that I use to get data or a parameter that the user input in the terminal.
This is my script.
<?php
$opt = getopt("f:");
$input = $opt['f'];
$u = fopen($input, 'r');
echo "\n\n$input\n\n";
I tried to run it like this:
$ php myscript.php -f http://myurl.com/file.csv?city=london&status=3
My url is http://myurl.com/file.csv?city=london&status=3, but it only outputs http://myurl.com/file.csv?city=london. The status parameter is lost from the full URL.
How can I get this to work?
it's because you have to wrap your link around into quotes:
$ php myscript.php -f "http://myurl.com/file.csv?city=london&status=3"
I'll go ahead and assume you are running your script in Bash, and & in Bash might be interpreted as bitwise AND in your case:
$ echo $(( 98 & 7 ))
2
I have installed SymPi in the server and from the command line, I am able to execute the following.
python ./sympy-0.7.5/bin/isympy
(this will open a console where I can type mathematical expressions. then the following expression)
1 + 2
(will give 3 as output)
My aim is to do the same from php using shell_exec. I have written a php file as given below, but is not working.
$command = escapeshellcmd('python ./sympy-0.7.5/bin/isympy');
shell_exec($command);
$output = shell_exec('1 + 2');
Can anybody help me to figure out why this is not working?
Please note that the following script works fine which just execute a python script and retrieve the output.
$command = escapeshellcmd('python C:\PythonPrograms\test3.py');
$output = shell_exec($command);
echo $output;
My guess is that the working directory (cwd) of shell_exec is different from the one you're in when you execute it manually.
Your working example specifies a hard path that will work from anywhere. Whereas your not-working example specifies a relative path (./ is the cwd).
Convert your call to isympy to give its full path on disk. Or figure out how to set the cwd of shell_exec.
(If this doesn't solve it, say more than "is not working." What happens? An error? What is the full text of the error?)
Each time you run shell_exec, it opens a completely new instance of the shell.
Edit:
You can pass a command for python to execute like this:
$expression = '1 + 2';
$cmd = 'python -c \'print "%f" % (' . $expression . ')\'';
$output = shell_exec($cmd);
This, admittedly is not using sympy, but for simple mathmatical expressions you may not need to. If you do, you would just need to import the library in the same command, like this: python -c 'import sympy; print "%f" % sympy.sqrt(3)'
I could manage the desired result in a different way.
Created a python script which accepts the expression as the command line argument , execute and display the output.
Call this script from php by passing the expression as the command line argument.
I would like to execute a shell command through php and display it in a browser. Is there anyway to do so?
here is my php code : [test.php]
<?php
$number=$_GET["num"];
$date=$_GET["date"];
$output = shell_exec('egrep -w '2012-09-01|974' /home/myquery_test/log/push.log');
echo "<pre>$output</pre>";
?>
When I run this(test.php) file from browser nothing shows up. But when i change the
$output = shell_exec('ls')
its working fine!! Why isn't the egrep/grep command not working??
The egrep command isn't working, because you're using single quotes as a string constant delimiter: 'egreep -w' <==> 2012-09-01|974' <==> /home/myquery_test/log/push.log' <==Just use double quotes in the string, or as string delimiters OR escape the quotes.
shell_exec('egrep -w \'2012-09-01|974\' /home/myquery_test/log/push.log');
shell_exec('egrep -w "2012-09-01|974" /home/myquery_test/log/push.log');
shell_exec("egrep -w '2012-09-01|974' /home/myquery_test/log/push.log");
And, to avoid not getting the warnings and errors that would have brought this issue to light when testing, set your ini to E_STRICT|E_ALL, and fix the warnings, rather then ignoring them. [teasingly: after you're done with that, you might want to consider accepting some answers]I see you've accepted a lot while I was typing this post up :)
Using variables in your command:
$output = shell_exec("tail -f | egrep '$number.*$date' /var/www/myquery_test/log/push.log");
$output = shell_exec('tail -f | egrep "'.$number.'.*'.$date.'" /var/www/myquery_test/log/push.log');
$output = shell_exec("tail -f | egrep \"$number.*$date\" /var/www/myquery_test/log/push.log");