changeset 99:07e803c77850 draft

Uploaded

--- a/ideas_genome_tracks.R	Fri Feb 16 10:40:13 2018 -0500
+++ b/ideas_genome_tracks.R	Fri Feb 16 11:17:39 2018 -0500
@@ -91,12 +91,12 @@
         track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
         write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F);
         cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed);
-        system(cmd);
+        run_cmd(cmd);
         track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
         cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed);
-        system(cmd);
-        system(paste("rm ", track_file_name_bed_unsorted));
-        system(paste("rm ", track_file_name_bed));
+        run_cmd(cmd);
+        run_cmd(paste("rm ", track_file_name_bed_unsorted));
+        run_cmd(paste("rm ", track_file_name_bed));
     }
 }
 
@@ -260,6 +260,13 @@
     return(track_file_name);
 }
 
+run_cmd = function(cmd) {
+    rc = system(cmd);
+    if (rc != 0) {
+        quit(save="no", status=rc);
+    }
+}
+
 # Create the directory that will contain all trackhub files.
 trackhub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
 dir.create(trackhub_dir, showWarnings=FALSE);