$ID = ""; } // Get data assoc. with this ID and reconstruct GDBnnn $gdbQuery = "SELECT DBname, Status FROM Genomes.xGDB_Log where ID ={$ID}"; $get_gdb = $gdbQuery; $check_get_gdb = mysql_query($get_gdb); global $DBid; while ($gdb_data = mysql_fetch_array($check_get_gdb)) { $DBname = $gdb_data['DBname']; $Status = $gdb_data['Status']; $DBid = "00" . $ID; $DBid = "GDB" . substr($DBid, -3, 3); $dbid = strtolower($DBid); } $job_name = "{$DBid}-{$DBname}"; $job_name_submit = job_name_strip($job_name); // display only; jobs_functions.inc.php; strip illegal chars ## Create dropdown using the current DBid (if any) as the "selected" option $gdb_dev_list = gdb_external_dropdown($DBid); # (jobs_functions.inc.php; POSTS id=ID) ## create program-specific app list dropdowns $gsq_apps_dropdown = apps_dropdown('GeneSeqer-MPI'); //jobs_functions.inc.php $gth_apps_dropdown = apps_dropdown('GenomeThreader'); //jobs_functions.inc.php ## Get GTH parameters for the GDB selected $param_query = "SELECT Status, Species_Model,Alignment_Stringency, Gth_Species_Model,Input_Data_Path from Genomes.xGDB_Log where ID= {$ID}"; $get_param_record = $param_query; $check_get_param_record = mysql_query($get_param_record); $param_result = $check_get_param_record; $param = mysql_fetch_array($param_result);
$input_data_path = mysql_real_escape_string($_POST['input_data_path']); // $username = mysql_real_escape_string($_POST['username']); $libfname = mysql_real_escape_string($_POST['libfname']); # $genomeFormat=mysql_real_escape_string($_POST['genomeFormat']); $outputPath = mysql_real_escape_string($_POST['outputPath']); //to be modified further before posting- see below # $transcriptFile=mysql_real_escape_string($_POST['transcriptFile']); $Species = mysql_real_escape_string($_POST['Species']); $wsize = mysql_real_escape_string($_POST['wsize']); $minqHSP = mysql_real_escape_string($_POST['minqHSP']); $minqHSPc = mysql_real_escape_string($_POST['minqHSPc']); $minESTc = mysql_real_escape_string($_POST['minESTc']); $maxnest = mysql_real_escape_string($_POST['maxnest']); $gsq_job_name = mysql_real_escape_string($_POST['gsq_job_name']); $job_name_submit = job_name_strip($gsq_job_name); // jobs_functions.inc.php; strip any user-added illegal chars // calculate file sizes $trans_array_est = create_input_list($input_data_path, "est", $dbpass); # calculate total file size - est (jobs_functions.inc.php) $trans_array_cdna = create_input_list($input_data_path, "cdna", $dbpass); # calculate total file size - cdna (jobs_functions.inc.php) $trans_array_tsa = create_input_list($input_data_path, "tsa", $dbpass); # calculate total file size - tsa (jobs_functions.inc.php) $gdna_array = create_input_list($input_data_path, "gdna", $dbpass); # calculate total file size - genome $genome_file_size = $gdna_array[2]; // for jobs database as total genome file size // Get processor info from database based on selected app_id (note: 'nodes' is not required, the app is pre-configured for node count, but we sent it anyway for informational purposes) $query = "SELECT nodes, proc_per_node, memory_per_node, platform from {$global_DB}.apps where app_id ='{$app_id}'"; $result = mysql_query($query);
$inputGenomic = mysql_real_escape_string($_POST['input_g']); //temp input path for Genome File e.g. /username/xgdbvm/tmp/GDB002_hpcs/SCFDIR/GDB002gdna.fa $inputProtein = mysql_real_escape_string($_POST['input_p']); //temp input path for Protein File e.g. /username/xgdbvm/tmp/GDB002_hpcs/Protein/GDB002prot.fa $gth_split = intval($_POST['gth_split']); $total_scaffold_count = intval($_POST['total_scaffold_count']); $Species = mysql_real_escape_string($_POST['Species']); $requested_time = mysql_real_escape_string($_POST['requested_time']); $admin_email = mysql_real_escape_string($_POST['admin_email']); $input_data_path = mysql_real_escape_string($_POST['input_data_path']); // $transcript_type = "prot"; //by definition, the only type for GenomeThreader $gth_job_name = mysql_real_escape_string($_POST['gth_job_name']); // already regex'd for illegal characters $job_name_submit = job_name_strip($gth_job_name); // jobs_functions.inc.php; strip any user-added illegal chars // reconstruct outputName $outputName = $DBid . "prot.gth"; # e.g. GDB001prot.gth // calculate file sizes (for reporting) $trans_array_prot = create_input_list($input_data_path, "protein", $dbpass); # calculate total file size - prot (jobs_functions.inc.php) $input_file_size = $trans_array_prot[2]; // save to jobs database as total protein file size $gdna_array = create_input_list($input_data_path, "gdna", $dbpass); # calculate total file size - genome $genome_file_size = $gdna_array[2]; // for jobs database as total genome file size // Get processor info from database based on selected app_id (note: 'nodes' is not required, the app is pre-configured for node count, but we sent it anyway for informational purposes) $query = "SELECT nodes, proc_per_node, memory_per_node, platform FROM {$global_DB}.apps WHERE app_id ='{$app_id}'";