To setthe  ini key phar.readonly to 0, from a unix shell script, this is possible on the fly it is possible see below.
The example given on this page has some issues with quoting: (See conversion to simple quotes)

#!/usr/bin/php -d phar.readonly=0
<?php
print(ini_get('phar.readonly')); // Must return 0
// make sure it doesn't exist
@unlink('brandnewphar.phar');
try {
    $p = new Phar(dirname(__FILE__) . '/brandnewphar.phar', 0, 'brandnewphar.phar');
} catch (Exception $e) {
    echo 'Could not create phar:', $e;
}
echo 'The new phar has ' . $p->count() . " entries\n";
$p->startBuffering();
$p['file.txt'] = 'hi';
$p['file2.txt'] = 'there';
$p['file2.txt']->compress(Phar::GZ);
$p['file3.txt'] = 'babyface';
$p['file3.txt']->setMetadata(42);
$p->setStub('<?php
function __autoload($class)
{
    include "phar://myphar.phar/" . str_replace("_", "/", $class) . ".php";
}
Phar::mapPhar("myphar.phar");
include "phar://myphar.phar/startup.php";
__HALT_COMPILER();');
$p->stopBuffering();

// Test
$m = file_get_contents("phar://brandnewphar.phar/file2.txt");
$m = explode("\n",$m);
var_dump($m);
/* Output:
* there
**/