Fixed missing slashes when using folders from settings.ini

imgag · Nov 16, 2024 · a29981c · a29981c
1 parent 9a82eaf
commit a29981c
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/NGS/mapping_star.php b/src/NGS/mapping_star.php
@@ -15,7 +15,7 @@
 
 //optional arguments
 $parser->addInfile("in2",  "Input reverse reads in FASTQ(.GZ) format for paired-end alignment.", true);
-$parser->addString("genome", "STAR reference genome index.", true, get_path("data_folder")."genomes/STAR/GRCh38");
+$parser->addString("genome", "STAR reference genome index.", true, get_path("data_folder")."/genomes/STAR/GRCh38");
 
 $parser->addFlag("uncompressed", "FASTQ input files are uncompressed.");
 

diff --git a/src/Tools/data_setup.php b/src/Tools/data_setup.php
@@ -96,8 +96,8 @@
 {
 	$base = basename($file);
 	print "  rsync-ing genome file '$base'.\n";
-	$existed_before = file_exists($local_data.$base);
-	list($stdout, $stderr) = exec2("{$rsync} {$genome_folder}{$base} {$local_data}{$base}");
+	$existed_before = file_exists($local_data."/".$base);
+	list($stdout, $stderr) = exec2("{$rsync} {$genome_folder}{$base} {$local_data}/{$base}");
 	foreach(array_merge($stdout, $stderr) as $line)
 	{
 		$line = trim($line);
@@ -106,9 +106,9 @@
 	}
 	if (!$existed_before)
 	{
-		if (!chmod($local_data.$base, 0777))
+		if (!chmod($local_data."/".$base, 0777))
 		{
-			trigger_error("Could not change privileges of local data folder '{$local_data}{$base}'!", E_USER_ERROR);
+			trigger_error("Could not change privileges of local data folder '{$local_data}/{$base}'!", E_USER_ERROR);
 		}
 	}
 }