# HG changeset patch
# User greg
# Date 1515007329 18000
# Node ID 55da56869a0d86c43670bec941df20624f025e47
# Parent 8c4549f123da3d0049e69e64c7929fc91e8a120e
Uploaded
diff -r 8c4549f123da -r 55da56869a0d ideas_genome_tracks.R
--- a/ideas_genome_tracks.R Wed Jan 03 13:59:17 2018 -0500
+++ b/ideas_genome_tracks.R Wed Jan 03 14:22:09 2018 -0500
@@ -26,20 +26,18 @@
args <- parse_args(parser, positional_arguments=TRUE)
opt <- args$options
-create_primary_html = function(output_trackhub, hub_dir) {
- hub_dir_files <- list.files(path=hub_dir);
+create_primary_html = function(output_trackhub, tracks_dir, build) {
+ track_files <- list.files(path=tracks_dir);
s <- paste('', sep="\n");
- s <- paste(s, 'Contents of directory ~/myHub', ' required by UCSC TrackHub
\n', sep="");
+ s <- paste(s, 'Contents of directory ~/myHub/', build, ' required by UCSC TrackHub
\n', sep="");
s <- paste(s, '\n', sep="")
- for (i in 1:length(hub_dir_files)) {
- s <- paste(s, '- ', hub_dir_files[i], '
\n', sep="");
+ for (i in 1:length(track_files)) {
+ s <- paste(s, '- ', track_files[i], '
\n', sep="");
}
s <- paste(s, '
\n\n', sep="");
cat(s, file=output_trackhub);
}
-
-
create_cells = function(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors) {
# Create everything needed, including the bigbed file,
# to render the tracks within the UCSC track hub.
@@ -219,4 +217,4 @@
write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
# Create the primary HTML dataset.
-create_primary_html(opt$output_trackhub, hub_dir);
+create_primary_html(opt$output_trackhub, tracks_dir, opt$build);