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run_now.php
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run_now.php
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<html>
<body>
<?php
if( !isset($_POST['code']) ) { echo shell_exec('echo ERROR: No code passed to run.php >> user_data/ERRORS/input_validation.log');}
$code=preg_replace('/[^A-Za-z0-9]/', '', $_POST["code"]);
if (!file_exists("user_data/$code")) {
mkdir("user_data/$code");
}
if( !isset($_POST['kmer_length']) ) { echo shell_exec("echo ERROR: No kmer_length passed to run_now.php >> user_data/$code/input_validation.log");}
if( !isset($_POST['ploidy']) ) { echo shell_exec("echo ERROR: No ploidy passed to run_now.php >> user_data/$code/input_validation.log");}
if( !isset($_POST['max_kmer_cov']) ) { echo shell_exec("echo ERROR: No max_kmer_cov passed to run_now.php >> user_data/$code/input_validation.log");}
if( !isset($_POST['lambda']) ) { echo shell_exec("echo ERROR: No lambda passed to run_now.php >> user_data/$code/input_validation.log");}
if( !isset($_POST['description']) ) { echo shell_exec("echo ERROR: No description passed to run_now.php >> user_data/$code/input_validation.log");}
echo shell_exec("echo user_data/$code/input_validation.log >> user_data/$code/input_validation.log");
$kmer_length = escapeshellarg($_POST["kmer_length"]);
$ploidy = escapeshellarg($_POST["ploidy"]);
$max_kmer_cov = escapeshellarg($_POST["max_kmer_cov"]);
$lambda = escapeshellarg($_POST["lambda"]);
$description = escapeshellarg($_POST["description"]);
echo shell_exec("echo $description > user_data/$code/description.txt");
$url="analysis.php?code=$code";
$filename="user_uploads/$code";
$oldmask = umask(0);
umask($oldmask);
// For old version:
// echo shell_exec("Rscript histfitdup_bothplots.R $filename $kmer_length $read_length user_data/$code &> user_data/$code/errors.log &");
// For new version:
// genomescope.R histogram_file k-mer_length read_length output_dir
// echo shell_exec("Rscript genomescope.R $filename $kmer_length $read_length user_data/$code $max_kmer_cov &> user_data/$code/run.log &");
// For 2.0:
// genomescope.R -i histogram_file -k k-mer_length -p ploidy -o output_dir
echo shell_exec("./genomescope.R -i $filename -k $kmer_length -p $ploidy -l $lambda -m $max_kmer_cov -o user_data/$code >user_data/$code/run.log 2>&1 &");
$new_dataset = array( "date"=>time(), "codename"=>$code, "description"=> $description );
$my_datasets = array();
if(isset($_COOKIE["results"])) {
// echo "cookie is already there, adding to it.";
$my_datasets = json_decode($_COOKIE["results"], true);
} else {
// echo "cookie not set, creating new one";
}
array_push($my_datasets, $new_dataset);
header('Location: '.$url);
setcookie("results", json_encode($my_datasets));
?>
</body>
</html>
<!-- <form name="input_code_form" action="run.php" id="analysis_form" method="post"> -->