Mercurial > repos > greg > ideas_genome_tracks

changeset 30:4c42188478a7 draft

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Uploaded
author greg
date Mon, 27 Nov 2017 11:15:22 -0500
parents fc6f39767c83
children de98a1b0be8b
files ideas_genome_tracks.R
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Tue Nov 21 13:23:28 2017 -0500
+++ b/ideas_genome_tracks.R	Mon Nov 27 11:15:22 2017 -0500
@@ -194,21 +194,21 @@
 contents <- c(paste("hub", opt$hub_name), paste("shortLabel",opt$short_label), paste("longLabel", opt$long_label), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email));
 hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
 dir.create(hub_dir, showWarnings=FALSE);
-hub_file_path <- paste(hub_dir, "hub.txt", sep="/");
+hub_file_path <- paste(hub_dir, "hub.txt", sep="");
 write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);
 
 # Create the genomes.txt output.
 contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep=""));
-genomes_file_path <- paste(opt$output_trackhub_files_path, "/", "genomes.txt", sep="");
+genomes_file_path <- paste(hub_dir, "genomes.txt", sep="");
 write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F);
 
 # Create the tracks.
-tracks_dir <- paste(opt$output_trackhub_files_path, "/", "tracks", "/", sep="");
+tracks_dir <- paste(hub_dir, "/", "tracks", "/", sep="");
 dir.create(tracks_dir, showWarnings=FALSE);
 track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label, track_color);
 
 # Create the trackDb.txt output.
-track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");
+track_db_file_path <- paste(hub_dir, "trackDb.txt", sep="");
 write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
 
 # Create the primary HTML dataset.