# temp input path for Genome File e.g. /username/hpcGDB002/SCFDIR/GDB002gdna.fa
$input_p = "{$user_input_base}Protein/{$DBid}prot.fa";
# temp input path for Transcript File e.g. /username/hpcGDB002/Protein/GDB002prot.fa
## Set validation style for input files
$valid_est_array = create_input_list($gsq_input_path, "transcript", $dbpass);
// generic; covers est, cdna, tsa
$valid_est = $valid_est_array[0];
$valid_prot_array = create_input_list($gsq_input_path, "protein", $dbpass);
$valid_prot = $valid_prot_array[0];
$valid_gdna_array = create_input_list($gsq_input_path, "gdna", $dbpass);
$valid_gdna = $valid_gdna_array[0];
$valid_out_array = create_input_list($output_data_path, "gsq." . $DBid, $dbpass);
# e.g. gsq.GDB001cdna, test for type in function.
$valid_out = $valid_out_array[0];
## Set return job estimates based on size distribution of gdna:
$scaffolds = calculate_scaffolds($gsq_input_path, $gsq_proc, $gth_proc);
# jobs_functions.inc.php
// return array($large_scaffold_count, $small_scaffold_count, $chunks, $remainder_size, $gsq_split, $gth_split, $scaffold_size_display, $gsq_split_display, $gth_split_display, $gsq_time_display, $gth_time_display);
$large_scaffold_count = $scaffolds[0];
$small_scaffold_count = $scaffolds[1];
$total_scaffold_count = $large_scaffold_count + $small_scaffold_count;
$break_point_count = $scaffolds[2];
$remainder_size = $scaffolds[3];
$gsq_split = $scaffolds[4];
$gth_split = $scaffolds[5];
$scaffold_sizes_display = $scaffolds[6];
$gsq_split_display = $scaffolds[7];
$gth_split_display = $scaffolds[8];
$gsq_time_display = $scaffolds[9];
$gth_time_display = $scaffolds[10];
}
####### Part IIC. Set data paths and filenames for Curl ########
## Specify TEMPORARY user input data paths with user's home directory as base - the pipeine creates this directory and deposits data there
$user_input_prot_path = "/{$username}/{$inputTopDir}tmp/{$DBid}_hpc/Protein/";
//e.g."/username/xgdbvm/tmp/GDB001_hpc/Protein/"
$user_input_scaff_path = "/{$username}/{$inputTopDir}tmp/{$DBid}_hpc/SCFDIR/";
//e.g."/username/xgdbvm/tmp/GDB001_hpc/SCFDIR/" (note: this dataset is already size-sorted by commands in xGDB_Procedure.sh)
## Construct input path and output name variables for Curl statement. NOTE: these are used by TACC so they are relative to iPlant Data Store user home page ($username)
$inputProtein = "{$user_input_prot_path}{$DBid}prot.fa";
//user's DataStore path, for json; Protein File, e.g. /username/xgdb/tmp/GDB001_hpc/Protein/GDB002est
$inputGenomic = "{$user_input_scaff_path}{$DBid}gdna.fa";
// user's DataStore path, for json; Genome File, e.g. /username/xgdb/tmp/GDB001_hpc/SCFDIR/GDB002scaffold
$outputName = "{$DBid}prot.gth";
// for json; e.g. GDB001prot.gth
// deprecated $outPutPath="$user_output_data_path"; //for json; e.g. /username/GDB001_hpc/GTHOUT/
## Calculate split count and scaffold number for display
$scaffolds = calculate_scaffolds($user_input_scaff_path, $proc_per_node, $proc_per_node);
# jobs_functions.inc.php
$gth_split = $scaffolds[5];
# this is for information purposes only, it is the split of segments we predict will be used
$large_scaffold_count = $scaffolds[0];
$small_scaffold_count = $scaffolds[1];
$total_scaffold_count = $large_scaffold_count + $small_scaffold_count;
############## Part III. Refresh access_token for Agave API #############
// A. First, get the OAuth App credentials for this user, VM:
$handle = fopen("/xGDBvm/admin/auth", "r");
$auth_error = "";
if ($handle) {
while (($line = fgets($handle)) !== false) {
$pattern = "/^" . $username . ":([A-Za-z0-9\\_]+?):([A-Za-z0-9\\_]+?)\$/";
# e.g. newuser:hZ_z3f4Hf3CcgvGoMix0aksN4BOD6:UH758djfDF8sdmsi004wER
if (preg_match($pattern, $line, $matches)) {
