$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}'";
